Conception 2 is also available on 3DS, and MGS 3 is available for 3DS in 3D (Not the HD collection, but something.
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If those are the only games you're interested in, then I vote 3DS. Why? The 3DS games are longer, and more abundant. Bravely Default and Fire Emblem are both 60+ hours, meanwhile something like Soul Sacrifice and Tearaway are 10-20 hours.
The way I see it, 3DS is better for full pledged retail games, where Vita is better for PS1 Classics, and PSN titles. Both have classic, arcade & retail games, but one is better then the other.
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Also some suggestions:
3DS: Tales of the Abyss, Resident Evil Revelations, Bravely Second, Monster Hunter IV, SMT: Devil Survivor
Vita: Tales of Hearts R, Grim Fandango HD
Multi: Zero Escape: Virtues Last Reward
What is with all the hate? Don't read GamrReview Articles. Contact me to ADD games to the Database 
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