JPCT-AE:
+ free
+ nice, neat feature set
+ best support I've ever seen for anything, patches are often available within hours or even minutes of a bug report (yes, it's crazy)
+ lighweight / full control
+ performant
- Android and PC only; I don't think Egon (the developer) has any plans to port to iOS
I don't really have a lot of experience with 3D modelling and have not used Android studio for JPCT, so I can't answer those questions.
Unity
+ multi platform (but you need Mac hardware to deploy to iOS device)
+ no setup code (but this minimal time saver can be neglected for anything but prototyping or very small projects IMO)
+ built in profiler
+ built in GUI stuff
+ nice integration of physics engine, if your game needs it
+ WYSIWYG editor (which is really only an advantage for protoyping IMO - I don't think any bigger projects make heavy use of the Unity Editor)
+ everyone and their grandma is using it (meaning there are a lot of answers online)
- not really free unless you don't care about a fat Unity logo at game startup
- really really heavyweight / limited control
- probably lower performance than JPCT, but I have no prove for that
- everyone and their grandma is using it (I am not a big fan of howling with the wolves, especially when it's about a commercial product)
- this may a personal thing, but in my opinion, Unity makes it too easy or tempting to write dirt-ugly code. It's not about the language (c# is fine), but about the overal structure of the system. As you do have previous coding experience, this is not too relevant, but I would not recommend anyone to start their programming career with Unity.