Mods are great, but they generally lack cohesion. I agree with OP. I wish that instead of passive upgrades and only a couple tower/ammo variants, the game had a deeper tower defense aspect.
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.
Some mods change biter behaviour to make them smarter, such as Rampant. Others change the entire gameplay loop, like Warp Drive Machine. The mod ecosystem is huge, and it's far too early to claim you know for sure it'll be boring.
RTS elements. It’s really tedious dealing with base defense and biter expansion prevention if you want to build a rail world type of base (and have the map for it). Artillery helps somewhat but the range is limited by radar arrays’ range.
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 :)
The pathing of the enemies in Mindustry feels somehow more like a classic tower defense game. I think they come from a small number of points and are primarily focused on your “town hall” type structure.
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.