Glad you enjoyed it!
1. Yeah it is frustrating to not be able to pick up sugar, but this is kind of intentional to model "drowning in water" so to speak.
2. Maintaining roots is part of the challenge of the game, but I agree it could be more fun/interesting; I'm looking at adding sugar transport, or maybe make roots not require energy but e.g. only hold 1 resource.
3. Yes accidentally building is very annoying, definitely want to improve it.
Agreed it gets a bit boring once the plant reaches sustainability; I'm thinking about end-game challenges that would really add to the fun. What do you think would be fun once you've reached that stage?