To directly answer your question - PvP gear is OK, but PvE gear is generally better.
A lot of it depends on time. If you can spend a lot of time running instances, then focus on PvE gear. If you don't have much time for instances, then split between BG and instance gear. Personally, I only had time to run instances 2x a week (Fri and Sat night). Gearing up with instance drops would've taken FOREVER - especially with my luck (took over 15 SLab runs to get chest piece). However, I can run BGs 3-7x a day, depending on how long they take. So I made a mix of PvP and PvE gear, and it worked just fine. Heck, the Holy Pre-Kara guide even has some PvP gear in it, so it's not all bad. :)