It'd be nice to have more enemy and tower variants, with certain types of towers working better against certain types of enemies - or towers that debuff enemies instead of hurting them. Maybe there could be structures that attract nearby enemies so it'd be easier to direct where attacks hit.
I think stuff like that would keep the tower defense stuff from loosing relevancy in the late game while staying fun.
Let me build a bunch of units, set up patrols, feed them with resources, and actively deal in an automated way with Biters thinking my land is their land :)
They’ve certainly got a lot of overlap, but Mindustry feels like a tower defense game that has a good factory builder added on, while Factorio feels like the other way around.
Anyway, two great games.