Mindustry is more "Tower Defence" focused. Waves of enemies attack and you have to build turrets to stop them. As the game progresses, you can build units which can attack the enemy's base - so it become a bit of an RTS game.
So there is a superficial similarity to Factorio - discover and unlock new things, build a base - but it is much more focused on the attack/defend paradigm.
Mindustry is still awesome though, especially considering that it's open source.
I find Mindustry layouts a lot less tedious compared to inserters everywhere and I greatly prefer the Mindustry conveyor flow controls.
I do wish Mindustry added another transportation layer where physical transport between sectors was required rather than generic space launches. It would give a much more cohesive feeling to the various levels.
The armored and plastanium conveyors prevent this.
Factorio is much more in depth on logistics and is a single "level". Takes 30-60 hours on a casual first playthrough.
Mindustry is a tower defense game that uses factory style base building as added spice.
Factorio is a base building game that adds some tower defense elements as added spice.