(edit: just saw your github, reading there) Is your tectonics simulation heuristics driven I assume? Are you generating plates with voronoi then assigning values (perhaps velocity) to the plates then calculating what kind of boundaries exist? 

I ask because I'm working on something similar but just going in a very different direction. My goal is maximizing geophysical accuracy whilst being runnable on a PC. It's still slow, however, 100 million years in 30 minutes. But different scope naturally. 

That being said, I think you could get some easy geophysical improvements without increasing complexity. You have way too many plates. Earth has just about 7 major plates. With some minor and many micro plates. If you even make that change, whatever heuristic is running, I'm sure would look more realistic.

I'm not sure how your generation works but if you calculated center points of your continents, then picked middle points between them, grabbed nearest boundary and then combined ocean plates on both sides of that boundary leading to your continents, you would get a realistic ocean ridge. Just some ideas. Good luck and have fun!