Honestly? If you're planning on using the Gateway and you have the cash to spare, get yourself a 64GB mSD for the 3DS slot and a 32GB for the red/blue card.
I say mSD because if you want to use it in a N3DSXL you'll need a mSD, but the adapter works for the O3DSXL and there *is a way* to use more than 32GB on O3DSXL if I remember correctly. (requires hacking?)
Just go nuts and get as many .CIAs and avoid ban hammer. The Gateway can even transfer savedata, so go nuts. Nintendo even has a cart>eShop savedata tool you can use for free, but Gateway is soooo much better.
For more moderately priced, stick to 32GB. Again, go mSD and use adapter, blah blah blah.
There's lots of reports on "fake" cards and certain manufacturer's not working, but really, if you know how to properly delete and rebuild an mSD it doesn't matter.
GET CLASS 10!!!! This is the only thing that will make a big difference. Some SDXC cards and "Ultra" cards are simply using UHS-1/3 that speed them up in a PC, but I'm pretty sure that's what causes most conflicts on the 3DS and Gateway and Sky3DS.
STICK TO CLASS 10!!!! Try to avoid UHS-1/3 and SDXC cards or "ultra" or "extreme".
Get a mSD>USB adapter. Most retailers include one with purchase.
Again, don't drop more $$$ than you need to. The more bells and whistles the more problems you'll have.
You want to aim for a BASIC CLEAN CLASS 10 SDHC mSD CARD.
64GB should be plenty to work with. But 32GB is so much cheaper. 128GB is expensive (like $100 worth of expensive) but man... imagine all the games and homebrew tools/apps. Problem? Most 128GB mSD are SDXC UHS-1/3. So you might have issues using them.
Here's a good place to do a little reading about SD cards:
https://www.sdcard.org/consumers/index.html