Mechanically, 2 was pretty sound. it introduced hold items, breeding, happiness, day/night, physical days, 2 new types, rebalanced some types and whatever else. it probably helps that it was originally a sequel to Red/Blue, but changed during development after noticing how much of a cashcow it became in merchandizing.
3 was disappointing just for R/S, sure it added abilities, natures and double battles, but it also simplified days to the extent that it was only used for Berries (which is its own scrappy mechanic) and TV shows...which rarely shows the one you want, purely to patch holes in secret bases, the aftergame was near non-existent, but that was pretty much a given, which might be why Emerald gets a Battle Frontier...doesn't explain why they always never include it in base versions of every generation than just adding it every 3rd game.
If you look at HGSS, now that was pretty awesome, berries was pushed into Berry Pots, the Pokewalker was quirky for potentially powerful or simply novelty Pokemon (Kangaskhan is the former...for a starting route pokemon), only major issues being that they forced the Moss/Ice rock to be Sinnoh-only and even stuff like Mount Coronet's Magnetism, forcing players to evolve their Eevee/Magneton/Nosepass in DPPla, on the upside, they made Feebas a bit easier to evolve before ultimately making it a trade evolution in BW.
BW was easy, Audino was simple to grind on, and most of the Pokemon were favorable, most non-Unova Pokemon had small movesets, but that's because TMs are reusable, forcing some creativity, BW2 was....weird, gave up at Elesa, but the Passerby Mall is potentially overpowered with EV training, Level boosting, Happiness groomers and oddities like a grab bag at a antiques shop or Master Balls...
EDIT: ONE small thing i don't like about Gen 3 is that Gamefreak had TOO much to work with, the Sprites in Crystal was fluidly animated whereas R/S just stretched, distorted or had some color glow rotation, making the animations look atrocious. also the sound sets of gen 3 just gave them too much to work with, which apparently translates to HORNS. R/G was in development for over 6 years before it came out near before the Gameboy died, so gen 2 was pretty much their apex in the music department.
Gen 4 uses more real music, but they're normally distinct based on the area they're in. Gen 5 seems more cultural to an extent.