Between Conan and TMNT I have experienced the whole gambit of sub-system sprawl. Conan was mostly a universal system, TMNT had a subsystem for everything (sometimes with rules inside of sub-elements of a subsystem). I still enjoy both methods, but I prefer more unified systems.
This was cemented when I played DC Heroes which had a universal system for everything. This is a great system for super heroes (I have used it quite successfully for Star Wars with Jedi as well). It avoids point sprawl (the difference in Strength between Superman and Batman is 16 points) and it supports Supers, Constructs and gadgeteers equally. And everything gets resolved on one universal table. It was later ported away from the DC license to Blood of Heroes. This is a great game system, it is out of print, but worth a try if you can find it.
When I am designing my own RPGs, I try to follow my preferences. I want there to be a single system to resolve everything in my designs.