I was not aware of "crosspathing" I see Baloons TD has it, I'll need to play that one. I was thinking about having different upgrades to choose from but that would be for the "master woodcutter". For the woodcutter I personally love the ability to spam more buildings with one button :D Regarding performance I think it should be doable (the game at it's current state has almost no optimizations made - it's a POC).
Regarding new threats and enemies - someone else already gave this advice, you could go old school stronghold style where you had both economic and military missions but the military aspect would probably be just an addition. Seems like a good idea - probably invaders similar to the bad north :)
Regarding the linearity of the threat what do you think about having some monks that would pray or something and that would reduce the flood level?
For difficulty, you could try to have 3 but it's up to you where there is peaceful (just no enemies and a relaxed gameplay), normal (enemies are present and flood rises a little bit fast), hard (enemies are much harder and flood rises fast). Definitely!
The "weights" system also make it have a feeling from those roguelike games so you could try to expand them, and don't feel afraid of going extreme for it. Funny you say that because I was thinking today that the current ones are not extreme enough and kind of "meh" :D
It's up to you to expand the game especially if you still focus on the woodcutting theme, it's only how it is much more like a one-win game so improve on that part and good luck! If I decide to develop this the next step would be a demo. That would require some serious work as I would have to probably start fresh since the current prototype is one big spaghetti with lots of cheese on top :D Improve the models (the ones you see are my first blender models), graphics and have at least 3 levels, proper UI. Plenty of ideas.
Thanks again for the comment! Every input is very valuable at this stage.