Great ideas! Thank you for sharing them :)
I would definitely like to increase the overall cat-ness of the game. Right now it's pretty weak.
Few points I'd like to comment on:
Giving the lander more purpose: Having it act as a low-tech workbench would be nice. I think the less items the game need to give the player at the beginning of the game, the better. I've also been scheming a research/science tech-tree feature. The lander might play a part in that as well. Not sure yet.
+1 for waypoint stuff without having to open up the minimap.
The player-input definitely needs an overhaul at some point. Especially for mouse clicks, which isn't consistent right now. There's lots of different styles of interactions that I'm trying to make it handle (equitable items, consumables, base modules, placing items on base modules, resource tiles etc), -- can't imagine it's very clear to new players.
Root plants I'm going to let players grow in the greenhouse, but probably not the trees (since they're an infinite source of food right now). Need to think about it some more.