As nice as 3D is on 3DS, it's nothing more than a gimmick. Few games seem to use it properly. HD is much better for your eyes and is cheaper to develop graphics for that resolution.

As SvennoJ already explained, the natural world is NOT stereoscopic 3D.  In the real world, objects at different distances have different focal planes, subsequently requiring constant refocussing.  In stereoscopic images, it's a single focal plane.  This is why too much stereoscopic viewing can be detrimental to young children who have not yet fully developed their sense of depth.

My only experience with 3D is the 3DS and a very small amount of games used the effect well. If every game had the quality of 3D as Lords of Shadow Mirror of Fate, then I'd prefer 3D over HD.

I'm plenty immersed already with a 92" screen :) HD makes a huge difference.
Occulus rift is cheaper though and requires far less room.

My main interest is the accurate head tracking, something you simply can't do right with a fixed screen. I always thought it would be awesome with FSX, landing a 747 in virtual cockpit view, then I realized you can't see the keyboard while wearing the rift... GT7 with VR headset will do, Star citizen with Occulus rift might work too, but space sims usually also require lots of buttons.

HD ... 3d is meh

This, so much this! LBW made me realize just how much I really wish there were more quality games with the 3D done right. The game's pretty without the 3D, sure, but the 3D really adds a lot to the experience.

Between the two, HD is less worthless.

HD in console and PC games, 3D in handheld games. 480 pixels or so is enough for a small screen, but 3D has yet to be prefected for the large screen.

like others have said... HD
3D is an after thought and shouldn't be the selling point of a game.
But with oculus/VR whatnot + HD would be best combo.

Also you can't play as much with 3D since it tires your eyes.

Still waiting for 4D...

How about HD VR. Occulus Rift ftw!