For technical detail, of what I’ve played, DK Returns.

My favorite visually, given that it had considerably large environments, is Pilot Wings Resort. I lived gliding ‘n riding through and around that huge island.

I always felt the Yokai series actually looked pretty great for a 3DS games.

Luigi’s Mansion 2. It also has the best 3D effect of any game, I love how every room looks like a small diorama.

Resident Evil Revelations.

I don't care that you excluded it. It's a beautiful game and it deserves the praise.

Other than that, I'm going to say Pilotwings resort. On a technical level, it's generally simplistic, but it's one of the best showcases of the 3D feature. I still play it now and then, primarily for the visuals, and that's not something I can say about a lot of games.

Kingdom Hearts DDD is a great looking game. Sticker Star for its faults is very pretty as the art style works well in 3D. Kid Icarus Uprising is also quite good. And, Luigi's mansion.

And... Xenoblade Chronicles. I mean, it sort of looks ugly, but at the same time, it's super impressive that they got the game to run on the 3DS in a relatively uncompromised form. The game was already pushing the limits of the Wii.

While I liked how RE: Revelations looked IMO the best looking 3DS game is still Luigi's Mansion 2, and I would also like to give a nod to 3D Land. All 3 are amazing looking games, and honestly, I could not decide which is technically more accomplished.

Captain Toad: Treasure Tracker was fairly good and easy on the eyes. Given it's a port.

No one has mentioned Fire Emblem series yet? Those battle sequences were life and death!!

And honorable mention should go to Metroid Prime: Federation Force. I forced myself to finish that game multiple times due to the wait time in-between for more Metroid, please...

Some less conventional options:

Beyond the Labyrinth: This one was never launch outside of Japan. And it's a shame, because it looked super good and seemed to have a very interesting premise:

Nano Assault: A downloadable game by Shin'en, creators of FAST RMX and The Touryst. For a 3DS game, I think it looks incredible

Captain Toad: Treasure Tracker: A superb port from the Wii U that holds up surprisingly well when compared to the original version:

Great pick; Shinen are technical wizards as far as how much graphical performance they manage to squeeze out of low end hardware, and at 60fps to boot.

Absolutely. I'm still amazed by the original FAST Racing on the Wii. Incredible graphics at 60fps... And it weights less than 50 MB. This people are wizards xD

Yeah Jet Rocket on Wii was a stunner as well, as were Nano Assault Neo/Art of Balance/Fast Racing Neo on Wii U, and the latter's Switch remaster.