Why not have a look at Game Maker? It seems to be the most recommended 2D Engine out there.
EDIT: Misread your topic. You are looking for a 3D Engine. Have a look at Unity 3D or Unreal Engine 4
Failing that, there must be literally 100's of engines to choose from. Have a look at the Engine db on devmaster.net
personally I would only use a modding editor to, well, mod a game. If you want to create something similar to XY, but with different graphics or slightly different gameplay, modding XY will give you a clear headstart.
On the other hand, it will limit what you can do with your product. Given that XY is not yet open sourced, only players that own the original game can play your mod. If its open sourced, you might not be allowed to charge any money for your product, depending on the license it was open sourced with.
And even if this all is not a problem, you will not be able to shoehorn SC2 into an RPG without a LOT of work... maybe just as much or more work than start that from a game engine like Unity 3D.
About the controllers: every game engine will give you functionality for mouse and keyboard inputs, don't worry.
And whats with that weird old school resolutions? I know a lot of people still play on old toasters, still, i'd concentrate on full HD for now. Good news is, resolution will be again highly configurable in most engines. Most modern engine are able to handle dynamic resolutions for windowed play and dynamic window resizing, so I wouldn't worry too much about that.
The only catch is of course, if you design your GUI, make sure the GUI system you are using can either scale with the screen, or you need to wrap the GUI system with some scaler classes of your own.