Crystal annoyed me a little bit because it was Game Boy color Only, and playing as a female was a joke (she was changed into a boy whenever you traded or battled with another game, even if it was another Crystal) but other than that it was fine...I guess...
Having always played on a GBC, I could not care less
Ruby&Sapphire = Wasn't backwards compatible with the older versions (although on a technological standpoint, it made sense...the GBA Link cable wasn't backwards compatible, although the GBA itself was). Caused a major stir when we found out that the sprites for the previous 251 were in the game, only to later find out we needed to play an ill concieved Gamecube game to obtain them...and it wasn't even all of 'em...only SPECIFIC ones. Needed to catch 100 different species to use Pokemon Box and/or Trade with Fire Red/Leaf Green. (I had to unlock a damn peripheral I spent money for...) Took out the Pre-Battle Animations for the pokemon after establishing them in Crystal. Also took out the real time, sure there was a clock, but the world had no day or night. These entries weren't TOO bad either...but so many hoops to jump through...(Blaziken is probably to this day one of the BEST Pokemon Designs ever, to me, though...)
Not only the link cable was incompatible, but the Pokémon system itself, with the ways the stats of individual Pokémon were calculated, underwent major changes, introducing natures and abilities, doubling the IV range (the random differences in stats between members of the same species) and replacing the old "stat EXP" system with a new "EV" system, changing the method with which a Pokémon raised with training is made stronger than one caught at a high level, leveled up with rare candies or through the day care.
I have never been much of a "gotta catch 'em all" fan, I usually catch only Pokémon I want in my team and Pokémon I can only encounter once, so the lack of Pokémon availability without trading did not bother me. Catching random Pokémon in R/B to get rewards from Oak's aides was annoying. The requirement for Collosseum, XD, FR, LG and Ruby in Sapphire is hardly different than requiring R/B/Y and Silver in Gold for Pokédex completion to me. Just more games and an additional peripheral that can also be used with other games. Plus, I never had a cube, so I could not play Cube games anyway. I have only had both of the main pair of games back with R/B, and never really played red anyway. Probably contributed to not getting Silver and later.
Fire Red & Leaf Green = Remakes...not a bad job getting it up to speed with third Gen...although it was funny how there were no darks AT ALL in it (Can't say there was no steel because Magnemite got the new Steel trait when Dark and Steel were introduced)...made sense though...they weren't around in Kanto...but certain moves got the new type priorities so that made some things interesting. HOWEVER, the number islands had the annoying trait of replacing how you got the National Dex...it wasn't an unwelcome quest because EXP is great, but I dunno...it was just kinda annoying that I had to beat the game to get it. Gold and Silver had the right idea with unlocking inter-generational trading HALFWAY through the game (read: after getting the first 4 badges), this way your older ones weren't rendered useless. Also introduced another useless nintendo peripheral in the wireless adapter...it was Game Specific, and not a replacement for the link cables (also had a strange feature that no one knew how to use. If you still have yours, try starting up your GBA with it attached, but either without a game, or with a game but holding start + select)...all they had to do was add a damn switch! Also wasn't compatible with the eReader battle cards from Ruby and Sapphire...missed oppritunity for EXP.
While Dark- and Steel-type Pokémon were not added to Kanto, moves were. With Bite turned Dark and Charmander learning Metal Claw, there were significant changes due to the new types beyond slight alterations in the matchup chart. With the National Dex, again I couldn't care less (actually I could, but it is not significant enough to break the game). Quite opposing your position, I think that the ability to trade over Pokémon from ye olde games in Gold might actually have been a flaw of the game. For the main storyline, relying on Pokémon caught in the very game you play is what makes it challenging. Sure, the badge restrictions for Pokémon obedience are there to prevent exactly that abuse, but GSC are probably the games where this system is weakest, as there is still much to do in the main storyline when you got the main set of 8 badges. While it is technically accurate that GSC had the weakest Elite 4, being able to trade over Pokémon from the completed RBY just made it worse. And because they are your own Pokémon and you did not have to beat a game of that generation even once to get them, the Kanto challenge is all but gone.
Emerald: Battle Frontier was the most awesome fuckup (yes, fuckup) ever. EVER. So many ways to battle! Learn old school moves! (FIRE PUNCH! ) Earn medals and items for your clubhouse...earn NOT ONE EXPERIENCE POINT FOR ANY OF YOUR EFFORTS!!! Fuck that noise. Also wasn't compatible with the eReader cards.
The Battle frontier is just like multiplayer battles in this regard. You do not get EXP for those either.
Diamond and Pearl = I figured out I got tired of the same old quest from game to game. It was cool that they brought back real time. The Poketch wasn't a bad addition. Pokemon types in this version weren't varied enough (where the hell was all the fire!?!), and a lot of the new features involved just didn't really grab me (I think this is because I'm a Veteran, but all that shit is awesome for first timers, I will admit). Also, transferring your GBA pokemon to the DS was a huge pain in the ass. You had a 6 per day limit, and then you had to CATCH THEM!?! Fuck...thats so retarded!
Yes, Fire was definitely underrepresented in Sinnoh, but that is largely due to it being a region up in the cold north. With the Pal Park thing, again, not my problem, and Platinum introduces many changes to remedy the dependence on old games to fill your Pokédex, due to the DSi's lack of GBA support. HeartGold and SoulSilver are also designed with a similar goal in mind, enabling you to get all 493 critters (minus the event-only legendaries like Mew, Celebi, Jirachi, Deoxys, Darkrai, Shaymin and Arceus, the four Regis, which can either be gotten from an event or via the old games and Manaphy and Phione, which are given from Pokémon Ranger) between D/P/Pt/HG/SS.
As far as I have heard, trading between HG/SS and D/P/Pt is available early in the game.