Most docs don't PvP well until they get to be rather high level, 150+ or even 180+. At that point, docs are rather hard to kill so the nanomage disadvantage doesn't seem as bad. On the other hand, if you get NT buffs, a doc doesn't tend to have nano problems, either.
Nanomages have an easier time casting all of our high level nanos. Solitus docs typically have to choose a nano route with their implant selection. However, if you're in a guild that holds a nice land control area (from notum wars) and you can get good towers up, then solitus docs don't have a problem here, either.
Just pick whichever you want.