But, if you think of it this way: Flashcarts atleast the 3DS ones, will always have a chance to get killed in the next update. And if it does, wouldn't games that require updates not work anymore? I'm pretty sure smash bros is one of them. (Forced me to update my old 3ds in order to play) I'm not sure if that is just a one time update though.
Also, can 3ds flashcarts use streetpass and is it safe? How about free dlc downloads such as MH4U?
Retail cards on the other hand will be worry free. They will never get blocked.
The thing that im most worried about flashcarts is that Nintendo will keep killing flashcarts until i pretty much spent on flashcarts equal to if i have purchased retail copies.
Nintendo updates sysnand, we play through emunand, which is safe from blocking the Gateway (as long as you dont blindly update). Technically Nintendo blocked Gateway long ago, but we still can play on latest nintendo FW because of Emunand. yes all dlc/updates/multiplayer work.
Fundamentally original DS was a closed system, only way Nintendo could block things is to release more sophisticated games that would detect if they were being run on real cart or not. They couldnt update the hardware to detect things. Things were much simpler.
These days 3DS gets regular updates, this will never change (at least until 4DS or whatever is released and 3DS is discontinued). There will never be a "future proof" cart, so no point in waiting for one, Nintendo can always block things (potentially), but so far they failed, and chances are they will never succeed. Stop thinking about the future proofing, because you never know, and will never know. And I am not just saying this.. litereally, there will never be a future proof cart (until 3DS is discontinued and Nintendo doesnt update it anymore), ever because of the nature of the system. It gets updated all the time. Instead see if its worth it for you at this point. In my opinion absolutely. There are at least 20 amazing 3DS games already, if you play 2 of them Gateway paid for itself.
partial list:
Zelda - Majoras Mask
Zelda - OOT
Zelda - Link Between Worlds
Fantasy Life <-- way underrated game by the way, its like Skyrim on 3DS AMAZING!
Animal Crossing
Monster Hunter 3U
Monster Hunter 4U
Code Name Steam
Pokemon X/Y
Luigis Mansion
Mario 3D World
Shin Megami Tensei IV
Smash Bros
Fire Emblem Awakening
Bravely Default
Etrian Odyssey Millenium Girl and IV
Mario and Luigi: Dream Team
Kingdom Hearts 3D
Paper Mario sticker Star
Mario kart
Kid Ikarus
etc etc list goes on...
All those work and will always work... just dont do stupid stuff like update your Sysnand.