You really don't need to save backups of every game you install. By the time something dies, you probably won't even want to play it anymore. If you do, it won't be hard to redownload or rerip the install files for the handful of games you actually still care about. Besides, nothing is stopping you from storing those backups on any USB drive you want. Buying an extra USB drive for the sole purpose of saving game installer backups is idiotic. Save those backups with the rest of your stuff, which would be on an NTFS drive. No, your SD won't wear out. It takes hundreds of thousands of writes to wear out. Writing 20 times for the good games, or 200 times if you insist on games you won't even play, won't wear it out.
I use a lot of SD cards and I've worn out many. None are Lexar, so I'm on a Lexar kick lately. SanDisks, Kingstons, Panasonics ... casualty count is high. And I know what you are thinking... fake or knock-offs. All bought from Best Buy. Lexars were bought from WalMart.
I've lost many saves for games I was actively playing on the 3DS when the SD card decided it had enough. Guess you are right about some games like Mario Kart where things are unlocked, you can just grab someone else's save file to unlock everything.
I use SD cards in all kinds of devices, like BananaPi Pro, Raspberry Pis, Cubieboard, etc. I've had a few cards go bad while in use on a 3DS, but those were ones that were previously used elsewhere already, so the 3DS itself wasn't the culprit of the wear-down.
About the comment about NTFS, not a windows user, sorry (not a MAC either). If I keep a local copy of my games on a hard disk, it would be on a FAT32, and it would be optimum to be able to plug that drive into the Wii U to re-install the games. The other backup of the games would be on a cloud service account. Otherwise, I can go ahead and to the work of transferring games to my SD card, installing, swapping out games as needed. Build up my Wii U USB hard drive, then 6 months from now for whatever reason I need to do a SYSNAND format and then that Wii U USB drive needs to be rebuilt. Then I got to redo copying installer files to a SD card, installing, swapping out, etc.
3DS games are smaller, so it never was an issue there, and I still have all the carts for the games, so nothing stopping me from redumping the games (fast enough process). But with some games exceeding 20GB on Wii U, USB hard drive support for installing becomes more critical.