I'm all for you differentiating your 4X from others. Although you may be torn on the issue of customization, just consider the grand-daddy of strategy games: Chess. No customization, with highly distinct role specializations for each unit. Yes, there are huge distinctions from your typical 4X (perfect information, limited movement constraints, etc), of course, but I think it's relevant to your concern about late game lack of choices. I find that lack of choice in a more strategy focused game can be EXCELLENT for master players because you know the constraints and can project your strategy much, much farther than in cases where there are too many permutations to consider. And it can be really satisfying when you master a strategic projection and follow it through its twists and turns until it finally works.
It's probably worth mentioning, though, that this will place a much greater emphasis on really strong AI or multiplayer support. I think 4X's with lots of variability, be it through unpredictable results that flow from zillions of ship options, or random events or whatever, can get away with less strategic coherence and depth. A game with less customization isn't going to have that benefit.