It's alright. If I were you (And I'm not, this is all personal preference) what I'd do, for flavor, is to get a bit of uniqueness by having "Primary" research nodes for sciences and smaller, cheaper nodes coming off of each for small selections of related parts. Sort of simulating "Science" and "Engineering". In general, "Science" nodes would have no parts or very few parts. This way, players would be able to skip parts they don't care about while still spending plenty of points to get good tech. They'll only save a few points, but you know how much of a difference that can make.
I do quite like the idea of later parts completely obsolescing older parts, simply being better - it adds a little extra flavor to the fact that ships you launch a long time ago will be much worse than newer ships. For instance, you might be able to get a flare projector early on with five flares, but later being replaced by a similarly sized but superior flare dispenser with twenty-five flares, lights becoming more efficient white LED lights, etc.
You could also make a bit of a unique tech tree type of thing by having tech radiate out rather than being in a straight tree. Maybe with Biology, Physics and Chemistry being your three branches (If you're going to split Research and Engineering like that). Certain parts or sciences would require you to get certain advances in all three fields.
I dunno, I'm just putting stuff out there. It might or might not conform to your vision, take whatever you like.