Is 60fps truly the desirable framerate over say 30? Most video you have ever seen was captured either at 24 (most films), 25 (some PAL) or 30 on rare occasions (typically news and sports) though we do have to take into account shutter speed there. Now throwing is 3d possibly changes things depending upon how they worked it.
Certainly I can think of scenarios where higher framerates are useful (fast pans for one though there are other more pressing concerns on non film stuff there) but as far as end user stuff goes...
I'd definitely say 60fps is a desirable framerate over 30. If lower is the only solution though, 30fps should be the absolute minimum. Anything lower is annoying. And with MGS3D, well just read my comments below as I respond in depth about that game. If I have the choice between a standard 30fps and something that looks much more smooth and fluid, i'm obviously going to choose the latter.
Myself though i'm particularly sensitive to low or unstable framerates. I tend to use PC's to game, but in the past I tried using a PC that wasn't powerful enough to handle a game's requirements. When the game would often drop below 30fps or so, I'd find myself feeling dizzy. In worse cases a headache, and in the worst case slightly nauseous. But a year years ago I upgraded to a better PC that exceeded the recommended specs, playing the same games at speeds well over 30fps (usually 60). I found that my issues were gone.
In regards to 3DS games that suffer from framerate drops, I've found myself fine during the smooth parts but can experience disorientation and dizziness when the game lags. I've had this recently with Kingdom Hearts 3D, which has an unstable framerate. In parts that stay at 30fps i'm fine, but when the game gets choppy I start to get a bit dizzy. If these scenes persist for very long I can get a headache (this btw is even without the 3D effect so it's not the 3D's fault, I don't have problems with 3D).
I'd say we're not too far off. A lot of 3DS games have frame rate issues or at least have moments where the frame rate obviously drops. I think Metal Gear Solid had trouble staying at 60fps.
Some games are just badly optimized though. SSFIV3D has some FPS issues while DoA;D stays at 60fps 95% of the time.
MGS3D is one of those badly optimized games. And it isn't even close to 60fps FYI. Hell it's not even close 30fps, the game has a maximum framerate of about 20fps, dropping off considerably from there. In fact the framerate will occasionally drop into the low teens and even single digits in places. Digital Foundry did a framerate analysis of the opening level and recorded it into a video (and the scenes they analyzed are actually during segments where the game runs at its best, later parts of the game suffer from far worse framerates than seen here)-
That's also not even mentioning the fact that with the exception of one or two extremely minor things, the 3DS version of Snake Eater looks considerably worse than its PS2 rendition as well. Normal mapping was added to some of the important character's models and in one instance during a cave segment the lighting effects are slightly better than PS2. But otherwise the game received noticeable and substantial graphical downgrades. Characters use fewer polygons than the PS2 version and a fair bit of the game's textures are worse quality. And during gameplay the foliage such as grass and other similar objects is far less dense than on PS2 and suffers from some pretty close-quarters pop-in (draw distance for foliage is only about 8-10 feet from your character).
This is not a matter of the 3DS being unable to handle the game though, it's more than up to that task. In the hands of better developers we could have gotten a game that both looked and performed BETTER than the original in every way. The 3DS is considerably more powerful than the PS2 regardless of the 3D effect. It's simply lazy development and poor optimization that is the culprit. Even the rushed tech demo shown at E3 called The Naked Sample looked superior to the final game in most aspects. And incidentally, the framerate of Snake Eater 3D isn't improved whatsoever by disabling the 3D, nor is there any anti aliasing applied like Capcom's games. So you can't blame the 3D for causing the performance problems.