Odyssey - It might be a hasty decision to put it here before waiting for the final version, but unless the ball is dropped incredibly hard I do think this is the best Pokemon fangame ever. Gorgeous, plays great, sounds great, tons of great ideas, everything, even a passable story for once. My only issue is something I think that really only hard mode with extra challenges suffer from.
Perish Song - Consider this, after a replay, the (now second) best fangame I've played. I think it hits every correct note on what it's trying to do, while also delivering a unique experience that really does a fantastic job at expanding on what Pokemon as a game can do. Difficult to the point of being tense but not to the point of being irritating and really sells the 'Souls but Pokemon' thing very well.
Clover - One of the highest effort and greatest projects really ever made from any fan community tee bee aytch desu fam. I really only struggle to put this one higher due to late game annoying maps and some of the fight design, but that's really it.
Emerald Rogue - Not just one of the best fan projects, but also I think roguelites period, with very few limitations other than the inherent ones roguelites have

Reminiscia - A cute, fun game with good characters and amazing art, one of the few fangames I wish was longer
Super Eevee Edition - An incredibly ambitious and high quality fangame that sets itself from the herd and is enjoyable to play, loses some points for lacking polish in certain areas
Ashen Frost - Probably has the best presentation of any fangame we've done, and maybe will ever do. Also is very unique and sets itself apart with the Ace Attorney case style gameplay. I do have an issue with the latter half of the story being fairly boring, some of the more annoying fights on hard mode, and some annoying design decisions like how grinding is handled, but I think these would be alleviated somewhat on a replay.
Desolation - One of the more paradoxical games in that a lot of what this game does is what we'd find annoying in other games, such as bad mapping or magical people babbling nonsense. However, it really does pull through with a lot of strong writing throughout, great major quest design, a solid but not over the top difficulty curve, and genuinely good story payoffs.
Realidea System - another cute and fun game that just loses out on higher positions for not differentiating itself greatly from '8 gym adventure' and also a spotty translation

Opalo - A game with a lot of soul and also a genuinely decent story that leads to an actually amazing climax and conclusion. Does miss out a bit for me personally due to being a bit too easy and more than a bit boring during the first region.
Tectonic - Plods quite a bit and is a bit more boring than I'd like. But it does offer a solid experience and changes up the battle system in a way that helps give it a good identity and has good exploration opportunity and mostly really good fight design
Apex - Generally well designed (outside of hard mode) with an interesting story and great presentation. Just could not stand some of the exploration or specific design choices that brought down the overall experience heavily, but hopefully will be rectified once the game pursues its own identity separate from Pokemon
Reborn - An incredibly well designed game, especially in terms of battles and side quests, and has a mostly coherent story. Suffers from an absolutely terrible cast of characters and incessant puzzlespam especially during the back half
Azure - It's a bit too early to place this high. But right now, has a general strong understandings of the fundamentals, with a few major mistakes that hopefully get ironed out in later versions.
Dimension Defender - Mostly competent and has a few very well done design elements, but not really that special
Gaia - Also mostly competent, but a bit less interesting overall than Dimension Defender
Concealed - has well designed maps and a very heartwarming/bittersweet ending, though very eyerolling a lot of the time. I think I put this a little too high on my last rendition of this tier list

Floral Tempus - It's decently entertaining, but suffers from a few too many gaping flaws in both storytelling and especially early gameplay, on top of not really having much of a solid hook
Unbound - It's well made, but tends to jerk itself off a bit too much over feature porn. Bad quest design and a pretty bad overall plot also bring this down
Bushido - Was very well made for its time, but nowadays the blatantly unfair fight design is more annoying to deal with than fun
Empyrean - Takes a major nosedive around the second half and gets too caught up in its own lore, and has some objectively terrible mechanics, but it has clear effort put in
Eon Guardians - stays far too much by the books to produce anything genuinely great or even noteworthy, but it's competent. This would be the drinking water of fangames
Rejuvenation - An impressive and ambitious game that just makes far too many mistakes and missteps both in-game and out for it to be recommendable in any real capacity

Saiph 2 - It's just a bland and annoying game at worst (which is most of the time) and generally okay at best. To be truthful, I like this one more than I should as it represents growth over the creator's two other games
Edelweiss Chronicles - Has one of the worst opening 2 hours I've ever seen in a fangame. The rest of it isn't as bad, but still has bafflingly garbage mechanics that drag it down even further on top of an incomprehensibly shitty plot. Only saved somewhat by really good looking maps
Insurgence - it's an old but pretty bad game. had decent scope for its day and did manage to deliver, but obviously pretty awful by today's standards
Void - Absolutely terrible dev-centered design philosophy, with the only thing saving this being that it's not very long and it has a good presentation
Saiph - This is basically just a soulless tech demo with barely any meat or anything remotely memorable on it. I guess it's passable for a minor first project but it's so nothing that I can't even really say anything negative about it

Empire - Fails in nearly every category to deliver a fun game due to a myriad of awful decisions that plague every aspect of the project. The only positive I can say is that it's not any of the below games.
Vanguard - Terrible writing and characters, terrible quest design, terrible mapping, this game is just barely playable. You go through maps that are so fucking bad that it makes you actively dread going into trainer fights because of how badly placed healing points are and then have to play through story segments that are less pleasant to sit through than bashing your skull on granite
Full Moon - How fast travel and padding are handled in this game legitimately made me want to kill myself playing through it. And that's before addressing the awful fanfiction plot that's actually insultingly bad or some of the worst mechanics I've ever seen in a video game period like the time gating shit.
Soulstones 2 - some of the worst design and gameplay I have seen in any video game. So unbelievably mind numbingly repetitive and boring, with a story that's the same tier of quality. Just incredibly painful on every level to the point that even though the kaizofucks are listed below, DemICE is not even somehow the worst part of this project.
Soulstones 1 - It's Soulstones 2, except it looks worse and the dev is a lot more inexperienced to the point of just stealing maps from better games. These flip flop only because I sometimes hate SS2 more when I remember the dev seemed to learn nothing at all from this dumpster fire.
Sors - This is a strong contender for the worst game ever made. I've played Superman 64 and I would probably play through that 10 more times before ever touching this shit again. The only reason it's even placed this high is because by sheer technicality I will give this 'game' more credit than the kaizomods below it (really, I don't want to make another tier), and because it isn't V***

SLLD Eclipse - All the kaizo games are here below the actual worst games because replaying the same battle over and over making the exact same inputs and making slight adjustments and hoping for not shit RNG isn't Pokemon, it's a shittier version of speedrunning and speedrunners all hate themselves and hate having fun period. Also, the talentless morons couldn't have even been bothered to attach their autism to an actual game they made themselves, but parasitize others. This one is the least garbage as it gives you a lot of variety, has a functioning difficulty curve, cuts out a decent bit of the RNG, and doesn't have Rejuvenation's baggage slapped on to infuriate the player even more
Urmumium - I really hate replaying Rejuvenation
Rejuv MM - I really hate replaying Rejuvenation

Diadem - Fun, looks good, solid grasp of the fundamentals, genuinely intriguing plot. Really hope this one goes far.
Last Chance - It's probably dead in the water, but at least it looked and sounded pretty good and seemed to have a fairly interesting premise.
Parabellum - Found it decently charming, even if it wasn't particularly fun and plagued by more than a few flaws
Bioterror - Nice presentation, but incredibly annoying to play. Hopefully that is fixed for later versions, or at least if the dev can figure out how to communicate better with the player.
Rosen - it's just way too fucking slow, and wasn't really interesting beyond that
Armistice - Annoying with a lot of fucked up maps. This game is already at 2 gyms but feels like it's in a worse state than when Reborn was at that point over a decade ago. With more polish and thought put into things like area design or boss fights, I could see this going places.
Repudiation - Terrible and outright broken mapping, buggy, no hook, fights weren't really fun, portraits looked pretty gnarly, just not much anything actually positive to this project and the dev seems very inexperienced to be handling a project of this alleged scope. Hopefully this develops to be much better.
Myth - I imagine if I ever replayed this it would go in D or F Tier, just horrible performance and story and gameplay

Virtualization - A legion of horribles, hundreds in number, half naked or clad in costumes attic or biblical or wardrobed out of a fevered dream with the skins of animals and silk finery and pieces of uniform still tracked with the blood of prior owners, coats of slain dragoons, frogged and braided cavalry jackets, one in a stovepipe hat and one with an umbrella and one in white stockings and a bloodstained wedding veil and some in headgear or cranefeathers or rawhide helmets that bore the horns of bull or buffalo and one in a pigeontailed coat worn backwards and otherwise naked and one in the armor of a Spanish conquistador, the breastplate and pauldrons deeply dented with old blows of mace or sabre done in another country by men whose very bones were dust and many with their braids spliced up with the hair of other beasts until they trailed upon the ground and their horses' ears and tails worked with bits of brightly colored cloth and one whose horse's whole head was painted crimson red and all the horsemen's faces gaudy and grotesque with daubings like a company of mounted clowns, death hilarious, all howling in a barbarous tongue and riding down upon them like a horde from a hell more horrible yet than the brimstone land of Christian reckoning, screeching and yammering and clothed in smoke like those vaporous beings in regions beyond right knowing where the eye wanders and the lip jerks and drools