Yes, you can simulate it as xcom did, but do note that it was extremely math heavy and not going to be very accessible for a beginner.
It depends on the scope of what you want to do really. Xcom actually simulated the path of the bullets and elevation and collision with intervening objects in a 2d engine. If you don't care about that then it should be significant easier.
killscreen.com/previously/articles/can-beautiful-beleaguered-isometric-perspective-make-comeback
As far as your specific requirement, no you won't be able to have 3d models in a 3d terrain. What you can do is like in Starcraft, model the units in 3d program, and export sets of sprite animations facing different angles to display in your 2d game.