Is it a nice idea? Certainly, the best thing about games for the PC is how tweakable everything is, and that goes quadruple for this game. Maybe it's something if you're really dedicated about you could mod into existence? Regardless, I think that unless it had been part of Alex's vision from the beginning it wasn't meant to be.
You're probably right about that. I have no coding ability whatsoever, so modding it in is not a possibility for me (even if I cared enough about it, which I don't, and had the time to spare for a project like that, which I also don't). It's fun theorizing about it, though.
I actually did try modding in 360 controller support several months ago in an attempt to add local co-op, and I can confirm that the game is borderline unplayable using a controller to pilot anything smaller than a cruiser for many of the reasons others have stated. I tried a variety of layouts and control styles, but the current flight control mechanics of Starsector just don't mesh with a dual-stick setup, even if at first glance it seems like they should.
The sheer number of combat binds also means that even if you limit binds to basic flagship control you will have to leave out
something important. It doesn't help that LWJGL has problems registering the 360 d-pad or when you press both triggers at the same time.
Surprisingly, one of the biggest problems with using a controller wasn't omnishields, it was flux management - specifically toggling weapon group autofire. There's no quick way to map that onto a controller, and when your flux is being driven up by enemy fire it's something you need to turn off as fast as possible.