To be fair, I was thinking more about 3rd parties, especially Japanese ones... even though, I think it's likely that for their next handheld, even that ship will have sink...
But then, it would depend of the shaders number. With 192 shaders, yes, they could go for 720p. For 128 ? then 540p. Finally, with 64 shaders, 480p.
In any case, that's up to what Nintendo is aiming for.
To be fair, a lot of their games could already fit a 3DS cartridge.
Wait, you think Japanese third parties won't be there for the successor of the (currently) only platform with a major installed base in the country?
Certainly, one of the things that Nintendo should guarantee is to get multi releases of mobile games, like Puzzle&Dragons, Million Arthur, etc.etc. I mean, not just the possible paid version for console audience (like P&DZ, which's been a big success on the platform, with over 1,5 millions sold), but the f2p, "original" versions as well. Currently, 3DS doesn't allow to port easily most of these games, due to its old architecture, so either they're not released or they're reworked. For example, Million Arthur came out just recently on 3DS, reworked. ...And, somehow, it's already over 200,000 downloads. F2P can work on 3DS already (at least download-wise): Initial D is over 600,000; Denpa Men Free is over 1,500,000.
Paid games as well, of course.
Nintendo should try to get them as near as possible to the release of the mobile versions, if not at the same time. No MS's parity clause, though...that does more harm than good XD
Also, if (as New 3DS is possibly an indication) 3D will still be there, I'd say 540p would be the best we can hope for, considering we're probably talking about a 5" top display at max. On 3D (thus, 1920x540), games should look great, correct me if I'm wrong.