BIGGEST GRIPE? It would have to be the seed storage! You should be able to keep seeds from every plant. If you had 1 slot for each seed and you could store as many of each seed in it as you want, that would be cool.
Second BIGGEST GRIPE? That would be a turner for pruning. On some of the plants you can't really see the dead stuff. If I could by a turner to spin them around, that would solve the problem. I know that one is asking for a little too much.