Titles like MHP, God Eater and Phantasy Star Portable, as well as Birth by Sleep and Peace Walker have one thing in common: they weren't possible to make on the DS in the form they eventually were released to. That doesn't apply with the next generation handheld war. The 3DS can certainly host competent renditions of MHP, GE and PSP, and is already receiving real entries in the MGS, KH and RE series that look and play well. Unless Japanese publishers decide that their future handheld games must sport HD visuals and the advanced gameplay engines that go with them (an idea I find flawed for many reasons), then there's nothing stopping the 3DS from gaining those crucial third party franchises that made the PSP a success. Meanwhile, Sony still won't have Mario and Pokemon, the two biggest handheld franchises ever, and if SE continues the tradition with DQ, then DQXI goes to 3DS as well.
It's not all just about money though, some developers just don't give a fuck. Kojima sees 3DS and says "stick a remake on there" yet sees the NGP and he's making a new game for the system. TBH is by the end of the year we don't have the usual MGS, FF, KH etc announced for the NGP I will be shocked for sure. It's already obvious what games companies will be offering for the NGP come release, immediately MvC3 comes to mind and also the RE game not releasing immediately on 3DS, that will go on NGP as well.
Mario and Pokemon ensure that Nintendo will always be top dog, just remains to be seen how big the gap will be between the 3DS and NGP. Of course there will be a new phenomenon next generation, always happens. Could be a current mid tier franchise which suddenly explodes such as MH did or something completely new, will be interesting to see none the less.