If you look at your .taskpaper file as something where you’re managing projects then Taskpaper gives you a cleaner interface to work with everything–for many of the reasons outlined above. PlainTasks, though powerful, doesn’t quite have the clean interactions. Focusing, filtering, searching, etc, are all easier to work with in Taskpaper.
It used to be that the search was quite a bit stronger in Sublime, but that appears to have been beefed up in Taskpaper. I guess the big difference is in Sublime you can search across multiple files at once. Depending on your structure, that may be a big thing.
If you do time tracking in PlainTasks I think you’d have to script something in Taskpaper to do the same thing, though if you’re comfortable with Java that shouldn’t be too hard ( I say that as someone who has only dabbled in java)
This part is subjective but to me Taskpaper lends itself better to organization and structure. PlainTasks becomes a bit more chaotic for me (which isn’t always a bad thing).
I mainly work in PlainTasks these days simply because I’m usually on a Windows machine. If I could have my ideal situation I’d work in Taskpaper and build in a time tracking facet like PlainTasks has.
If you’re always on OSX there’s no reason not to give Taskpaper a solid try for awhile. The files are compatable between the two programs so there’s no loss with whichever you go with.