This might be kind of a stretch (or just a bad idea), but: would it be possible to add a tool that nudged/aligned quad edges to parallel/perpendicular to the stroke direction as you go over them? Sort of like the relax tool, but directional, I guess.
In my head, this seems like it would be a good way to manually clean up topology, especially at lower mesh densities, as you could stroke along where you’d want an edge loop to be, and at least get edges more or less there.