I'm sticking with my Paper Mario prediction as in my E3 mystery thread. I could see another one being mentioned at E3 this year.
I also think that if F-Zero and/or Star Fox do not have a showing, then that means Nintendo is disinterested in those franchises and we may have to wait many more years until they are rebooted in a Kid Icarus type fashion.
The 3DS front is sort of interesting. It should be the more profitable division with titles able to sell a whole lot more due to a large userbase. Moreover, unlike the Wii U, development time for titles should be less thereby making it the more desirable system to be designing games for. Of course, the Wii U needs games so just how many titles will Nintendo want to focus on making for the system. Plus, nearly every franchise has now been represented on the 3DS with a couple of exceptions. Metroid, F-Zero, Wario and Advance Wars are the ones that spring to mind. Smash Bros. is coming along with more Pokemon titles in the Ruby and Sapphire remake. Will that be enough for Nintendo?
Last year, when everyone was raving about the 3DS it was carried by 5 big titles from Nintendo (LM:DM, FE:A, AC:NL, P:X/Y, LoZ:LbtW) although there were other notable release like M&L:DT, MP:IT, and DKCR. This year, it's had Yoshi's New Island, Mario Golf, Kirby and will have Smash Bros. and Pokemon. Will we only see a couple other titles added? Would a Majora's Mask remake seem likely to add to this list? With the line-up this year, it would seem to fit. Maybe development time would be even less for it than a brand new game. Whether it happens or not, I'd still say there's a good chance we see another Wario game (either Warioware or WarioLand) with maybe an Advance Wars announcement for next year. Other than that and another Mario sports title of some sort, I don't expect much else to be mentioned for the 3DS as I think we'll see more of a focus on Nintendo righting the Wii U ship.
Ultimate fan fantasy: a new 2D Metroid, a Drill Dozer sequel, a new Wario Land game and a new Advance Wars with Sega announcing a sequel to Rhythm Theif and Capcom announcing an E-Shop release of Ace Attorney Investigations 2. If that happens and Nintendo maintains the quality level that most of their 3DS titles have had, then this generation is over. 3DS won.