TMs being reusable and not disposed of after one use (which is what they should have been since Gen 1), Repels and their ilk renewing semi-automatically (from Black 2 and White 2 onwards), the dust clouds, rippling water and rustling grass, Black City/White Forest, the stadiums in Nimbasa City, and being able to challenge the Elite 4 in any order you want instead of a fixed order as in previous generations.
I absolutely loved Join Avenue. My group of friends in high school would always keep tabs on each other with it. It was really nice to keep things personalized.
Black City/White Forest. Having the ability to catch more non-Isshu Pokemon or battle more trainers in Black/White was great.