R&D might be nice, hopefully it'll come out first. Though that might not help me since I'm not in a ship building faction. I was thinking of modifications to existing ships more than anything. Still we'll see what comes up :).
Combat unfortunately I think is gonna be a real hard transition. The advantage is so great to some people at this point that when it comes out I see real problems. I know most would probably oppose it, but I would probably do a server reset at the onset of combat. Still we'll see maybe I'll be wrong, I hope so I just have a bad feeling about it.
Not being in the know, I'm only guessing, but I expect when R&D and combat are enacted you'll be able to have your ship modified for a price of course. Here is why I believe so. First off with combat, you'll have damage and possibly destruction of complete modules. So removing and replacing modules would be possible, making modification possible. And we'll have to see when R&D comes out, but I expect the ability to create and upgrade modules and thereby ships will be possible.
Warning this is strictly Orions McPhees Opinion, it may or may not have any bearing on events true or imagined
Teya I was mostly looking at perhaps higher hyperspeed maybe slightly better weapons nothing major. (After all the game version of the YT-1300 is really already modded, its based on the Millenium Falcon which was a heavily modified one :) )