Yes, that is the exact feeling I felt when I used to the 3D for an extended time. What usually fatigues my eyes that little sleep and a long day of work, reading and writer, happened in maybe an hour or less of playing with the 3D on. As cool as the 3D effect is, the slider is probably going to remain off 95% of the time.
I don't get the beef with the dpad. It's better than any DS dpad and only the location is awkward for me. I don't mind a small dpad if it has a nice roll and height (why I really like the GB Micro one).
And Resident Evil Mercenaries looks great and definitely on another level than what you see on the PSP. But it's mostly the sheen and added visual effects that make it look nice, so much the models or anything, which do seem comparable with the PSP. And I don't know if the laser sight is solid as a design choice or because the 3DS has trouble with transparency. In some pictures of Zelda 3DS, the water looks like solid paint.
They've also announced that RE Mercs comes with a demo of RE Revelations.