I think these games will be remembered for their great storylines and large, explore friendly region. The plot with Team Plasma in the games was far more in-depth than in games past and really set the tone for future games after it, as seen in Gen VI now. I also enjoyed how large the region and how many areas i could explore, especially post-game.
The most memorable part for me was in my Pokemon Black and at the Pokemon League, the Castle rising up and knowing that this was how it was going to end, my character against N, Reshiram vs Zekrom. That cutscene was one of my favorite all-time. There really isn't anything i personally want to change without going into a page and a half long analysis that is related more to how Pokemon in general can improve and change, not just Pokemon Black. I think these games were a step in the right direction and were a good stepping stone for Gen VI to build off of, which they have.