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New games:
>Prism (Gen II)
Has two entirely new regions, bits and pieces of a third + Kanto and Johto, 60 FPS, trainer customization, and adds new mons from later generations. Infamously was so high quality that it got C&D'd by Nintendo.
>Unbound (Gen III)
Entirely new region, all modern battle mechanics and every single Pokemon up to PLA, tons of QoL features, DexNav, sidequests galore, difficulty settings, expanded post-game with multiple facilities with multiple rulesets (Battle Tower, Smogon, VGC, Inverse, you name it). Extremely high quality but be warned that there's some lame stuff in there too (DUDE WEED LMAO).
>Glazed and Gaia (Gen III)
Both have new regions and bring in some newer Pokemon, but they're a bit outdated by modern standards when compared to Unbound. Glazed in particular was similarly C&D'd like Prism.
>Vega (Gen III)
Considered the premier Japanese hack. New region, but rather than bringing in new Pokemon, it has a number of fakemon that all fit the style of actual Pokemon. Again, a bit dated but it's still pretty fondly viewed.
>Clover (Gen III)
le epic funny 4chan hack. Brand new region with an entirely brand new Pokedex, consisting of hundreds of new designs, all designed by /vp/. Comes with level caps so the game isn't a complete pushover like the normal games aren't. Your mileage will strongly vary based on how well you can stomach 4chan memes; I've seen people consider it the best hack of all time and seen people consider it complete garbage.
Revamped games:
>Red++ (Gen I)
Gen I with improved graphics, sound, Gen II features, the ability to catch every Pokemon, new areas, backported mons, Phy/Spe split, bugfixes, the works.
>Crystal Clear (Gen II)
Crystal but open world. Sounds great on paper, but the OC shit can be hard to stomach.
>Polished Crystal (Gen II)
Essentially Red++ but for Crystal.
>Drayano hacks (Gen III-VI)
Difficulty hacks that allow you to catch all Pokemon in that game's dex.
everything else is either a WIP or shit