After a bit of searching, I think this might be a "commonly repeated but not actually true". A few people saying no, most weapons go 2d when you aim throughout the game, and a couple stay 3d throughout.
Sure. There were plenty that liked it. The technology was divisive, at the very least, and complaints of headaches were fairly common. I would say my personal group of gamer friends was probably split 50/50.
The original 3DS and 3DS XL gave me headaches. Whatever they tweaked with the New 3DS XL made it much more manageable because it does some adjustments with face tracking.
The original 3DS was definitely a "hold it at the right angle and keep it there" while the New 3DS tracking allowed for a lot more flexibility with how you hold it for the 3D to not be disorienting.
My problem with my New 3DS XL is that the power button is right where I put my pinky finger when using the shoulder buttons so playing Super Metroid sometimes ends with me "setting the 3DS down" on a desk while playing it, and my pinky bumps the power button which immediately autocloses whatever app you were running. Maybe there's a config option to not do that lol
The aftermarket has always done more for Nintendo's handhelds than they themself have. Aftermarket LCDs make the GBC and GBA truly enjoyable gaming handhelds versus the nigh-unusable messes they are out-of-the-box.
The Switch is probably the only real exception, currently; but I could just be ignorant and there are much better mods for it.
Last Christmas I replaced my old GBA screen with an IPS panel, and holy cow it is like night and day. It made me truly realize how powerful the GBA was, and how beautiful the games could be.
Back in the day we played the hell out of them because we didn't have anything better, but the original screens were truly awful even for their era.
Thus why the 2DS undercut so many sales for the 3DS.