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.
After a combined 1000 hours between the two, I find Factorio easier and much more satisfying. Factorio's base building is very explicit, while Mindustry's is very limiting. The main reason for me saying this is that in Mindustry all production buildings output their goods in all directions which makes it really annoying to design efficient layouts. It's also harder to play co-op in Mindustry because the maps are so small. Maybe my preference would be swapped if I had played Mindustry first rather than Factorio, but whenever I play Mindustry I think "wow I'd rather just play Factorio".
Mindustry is still awesome though, especially considering that it's open source.
> The main reason for me saying this is that in Mindustry all production buildings output their goods in all directions which makes it really annoying to design efficient layouts.
The armored and plastanium conveyors prevent this.
Mindustry encourages compact designs due to limited space in levels where factorio has infinite space that encourages sprawling designs. In that context, the all-side output is critical for Mindustry's compact layouts.
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.
In mindustry you build smaller factories, mostly to power turrets/build units to attack an AI. Focus is on tower defense. Logistics is cute but minimalistic. Each level takes 30-60 min on a casual play though.
Factorio is much more in depth on logistics and is a single "level". Takes 30-60 hours on a casual first playthrough.