I mentioned this before in another thread about this game about a month or so back...
We're likely to see some pretty decent framerate jumps before final game release... Simply because when you port a game, you're basically working BACKWARDS from what you do when you design a game from scratch for a system.
That is, when you first design a game for a specific system (say, Kid Icarus Uprising) you spend the entire first part designing graphics, engines, etc only with that system in mind. It allows you to push the hardware greater because all of the graphics were planned with it in mind. As the game comes together, it's likely very riddled with bugs and the last few months of programming are not as much about the game content/look as it is stability.
When you port a game, you go the other way around. Your first goal is to get the game running and stable on the system you're porting to. There is little reason in planning stages to rework the graphics till you're sure you can get them to work at all, and even then the whole goal of porting is to do as little extra work as possible. It's only after the game is up and running fairly stabley before you mess with the graphics engine to try and get it to the framerate you like.
The main issue here isn't that the 3ds is weaker than the PS2 (it's not) but simply how the PS2 renders it's graphics versus the 3DS. The 3DS' pica200 graphics are at least partially OpenGL ES compatible (designed to work similarly to other portable devices and, to an extent, PC hardware). The PS2 on the other hand uses what are known as VU's (Vector Units) which don't work like traditional PC hardware hardly at all. Yes, they have the same 'end results', but their method is very different and thus not optimized initially for the 3DS.
This would be different from say porting a Gamecube game to the 3DS. Like the 3DS the GCN's graphics card is semi-OpenGL compatible and works very similarly to it's PC counterparts (it was, after all, designed by ATi). The similaries to how they render objects would mean less optimization would be needed.
By the time MGS3D comes out, it'll have had the benefit of a lot more time and effort on their engine and we'll surely see a better framerate... Or at least I'd hope very much so... We've moved on from the era of 15fps gaming, I don't plan on ever going back.