I believe Vita went up is because there was a special sale in Japan that ended in the 31st that would give customers that bought a Vita 2000yen on a memory card. After it ran out Sony decided to extend the promotion.
Still... its only 2k up, not comparable to the numbers and rise the 3DS got.
Kingdom Hearts numbers were below what i was expecting, though in comparison BBS came out much later in the PSP life cycle and days on the DS life cycle (especially BBS that released only a year and a half ago). We wont know unless they release yet another one down the 3DS life cycle.
Maybe its actually good sales, or maybe the 3 giants are just eating up every other game that is launching. It seems like the japanese are pretty happy with just mario/mariokart and MH3G.
As far as development costs go, the engine used by 3D is supposidly the same one that was used for BBS so no doubt SE will make good money off it. Its not like releasing on the Vita would be a better idea at this point, the PSP could make a profitable port without the 3D.
