-They completely got rid of a lot of my gen 2 favorites. Remember, initially a lot of pokemon were unavailable, much like how when X and Y came out. So in my mind, I thought they were outright replaced and gone forever.
-I couldn't transfer any Gen 2 pokemon. I thought it was great how I could send my team from red and blue to gold, silver and crystal. So many pokemon I had an attachment to, and suddenly.... BAM I can no longer have them.
In the end, point one was remedied with future game releases, and I eventually got over losing all my gen 2 pokemon. Well I actually used a cheating device to recreate them all but that's besides the point.
Oh, I also thought the whole nature and ability thing was overwhelming.
Anyways, looking back, I can see they aren't nearly as bad as I believed them to be. I'd enjoy a remake so I can play them with my "anti Gen 3" thoughts.