I posted this on Reddit as well, but wanted to include some link back to these forums so others that don't watch Reddit can also see this information. Basically my issue was core parking, and disabling it completely eliminated my purple spikes shown in the FPS graph. (/fpsgraph 1). Granted I still see one or two every now and then, but it's 100 times better than the frequency I was experiencing them (every second or two)
https://www.reddit.com/r/sto/comments/44yd2u/psa_solved_my_stuttering_performance_issues_in/
You can find much more information at the link above, hopefully it will help some of you out! I banged my head against the wall for a few days trying to isolate this, the omega particle gathering really exaggerated the stuttering and hitching I have experienced for over a year now. Perhaps with this information in hand the developers can make some tweaks to the game engine to disable parking while STO is running, here's hoping at least.