GSC or HG/SS
1. You can really see the transition from the first gen, I have played the original Pokemon Red and Crystal versions.
2. The first gen was referenced a lot in the 2nd gen with easter eggs and professor Oak of course and other stuff, Then came the Kanto Arc which really made a connection with the first gen, you can feel that the game is not a game anymore, It became a new world.
3. There's "progress" in the story line. not just the GSC story line but the Pokemon story line as a whole, GSC is actually the sequel of RBY and if you compare BW2 and GSC in terms of playing the role of a sequel. GSC would pwn BW2.
4. You can feel the connection of a pokemon and its trainer, this is because all of the new content is centered around pokemon-trainer relationship. Unlike new contents these days that only caters to those who wants something new, im not against it but i just prefer a game which emphasizes pokemon-trainer relationship. and I think it shows especially when they did a remake (HGSS
wherein your pokemon actually follows you.
5. the battle with red at Mt.Silver is the best trainer battle ever in the history of Pokemon, Red was the only main character that appeared in tons of other generations and GSC started that formula.
6. the key ideas here are that GSC showed progress, TONS of progress in terms of EVERYTHING (contents, gameplay, core value, STORY). Its the only generation where a new typing was born, IIRC it started the dual typing, it also started giving genders as well as breeding and egg hatching, and it was the only generation where you can grab 16 MFKKING gym medals.
the list goes on and on, sure DPP and BW have these innovative contents, but the question is are they really necessary? did they pack that much impact to the whole picture? Battle Frontier was nice, The subway etc etc, but they had no lasting appeal on me unlike the GSC which really made me look at the pokemon series differently.