If you're fine using an older version of Retroarch, you can download the 1.6.7 stable version, which comes with separate core VPK instead of one VPK for all cores.
http://buildbot.libretro.com/stable/1.6.7/playstation/vita/ <
Download this, unzip, and choose the cores you want to use for an emulator. Be warned, however, that there may be some small bugs and issues and things that may not work that updated versions fixed.
Is there any particular reason you don't want to use just Retroarch's AIO version? I've been using it for ages and I've never come across any issues.