I have taken a look at Prison Architect and read through your concerns.
[quote:1ionjnwm]I'm wanting to create a game, I suppose it would be similar to Prison Arch in a way, with multiple units and the ability to build rooms and asortments within it.
Drag and drop behavior and grid would allow modular building pretty easy out of the box but you may want to event build your own building system as well (which is totally doable in C2)
[quote:1ionjnwm] Would this engine be able to support a large quantity of units with seperate commands (Assuming the AI is good)?
Yes. The AI in PrisonArch looks like a pretty basic logic tree.. no prob in C2. Large numbers shouldn't be too much of a problem unless your launching on older mobile devices. But there are lots of tricks to keep things from bogging down.
[quote:1ionjnwm]Would I be able to have seperate menus for things such as research and worlds maps? Can I set up a nice UI with the corrisponding buttons?
Yes, and Yes.
[quote:1ionjnwm]Can the tiles be reduced in size for a smoother look? (This was mearly because of what I've seen the tilesets seems very blocky and I was after a more smoothed non-pixelated look)
I haven't used tilesets but from what I understand you can use whatever tiles you like to get whatever look your after.
I would suggest like the first poster that you play around with Construct2 event making for a few days and make sure you like "programming" in it.
I will add a personal note as well... I have used basically all game making software out there over several decades (starting with programming in Turbo basic http://en.wikipedia.org/wiki/Turbo_Basic)... some examples... game salad, game maker, stencyl, craftstudio, blender, unity3-5, rpgmaker, etc. I like programming in code but I like the ease and organization provided by visual options more. I ended up in Construct2 for two reasons. I love the event making system of "coding" it is soo much easier than game makers version or stencyls visual scripting or the 2d in a 3d environment of unity. The second reason is the active community and ongoing development with very active devs.
All that said: If I was going to build a Prison Arch game I would build it in Construct2.