Currently, the 3ds is a solid buy. You've got the entire library of DS titles and some quality games like Threatrhythm, Super Mario Land 3d, the upcoming Project X Zone, etc. Between the price cut and the growing library, it's becoming a very well established system with an optimistic future.
The vita will honestly depend on your personal circumstances. Buying it new will cost you $250-300, plus $20-100 for the memory card (you'll want to spend at least $60 for the 16gig card). On the other hand, buying used on ebay you could get it for half that or less. Mine was $150 with a memory card, for comparison. So it can either be way too much or nice and cheap.
As far as the game catalog goes, it's a little lacking right now in terms of exclusives. Soul Sacrifice is one of TWO new games people are excited for this year on the vita, the other is Muramasa Rebirth. The lack of new exclusives makes the Vita's future a little dicey. Most of the hit titles on the system so far are big-name ports, like Atelier Totori and Persona 4. And the library includes the psn offerings of almost all digital psp games, psone classics, etc. So the system could offer you very little if you already have a ps3 and psp, or a lot if this is your only sony console.
In answer to your latest question, you can connect your vita to your PC or PS3 to manage it, or you can just go online with it and access the store to download titles. The store does not have a great library for tracking your purchases fyi. Once they download, you can just freely move them around on the Vita's menu screens.