Welcome to the club! I disable the 3D effect on maybe half the games I play: either they don't really need it, or the effect isn't visible enough to be worth it. Others really do use it well.
I'd have recommended Super Mario 3D Land if you didn't already have it, it's definitely the best portable Mario game I've seen in ages.
If you like rhythm games, or even if you don't, give a look at Theatrhythm Final Fantasy. I dropped from the main series at IX, but the music stays solid even through the titles I haven't played. There's a demo in the 3DS eShop if you want to give it a spin, that sold me to the concept. I spent an insane about of time playing it.
Kid Icarus: Uprising is a gem that I don't see recommended enough. At the risk of reusing a word that the Internet abuses way too much, I'd say it's the most epic game Nintendo has done in a few years. Some people have issues with the controls, but they didn't bug me at all. The production values are through the roof, and there's a lot of gameplay to be found.
If you liked Star Fox 64, the 3DS remake is basically perfect. It's prettier, the 3D effect works really well, and they didn't mess with the formula.
Right now, I'm still playing through Project X Zone. 40 hours in, and still having fun, although this one might not be for everyone!