depends on the game
in City Folk I loved tulips, they just looked really good and their colors were great, but I feel like they got a major downgrade design wise in NL and don't look anywhere near as good.
in Wild World I really hated cosmos because i thought they were the ugliest thing I'd ever seen, but in New Leaf they actually look pretty decent.
Idk my overall favorite from all games would probably be roses. I also really like carnations but since they've only been in CF and NL, I think roses should take the top spot due to being in all games.
At first, I really liked the roses in the game (I still love the pink and black ones) but I've been really liking cosmos for a while. It's a shame they aren't that popular. I also like the lilies. And honestly, my least favorite are the pansies. I'm surprised there are a good number of people who like them.