Without adding that these new games may require a Firmware update that will block the flashcart ... And i guess that we can't remove the update because then it would be unsigned code. So : We are screwed

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Now these are all ifs....first off if Nintendo can detect it then they can block it, but if they can block it then with a firmware update the cart can likely be activated again (just like DS flashcarts have been doing for years). Also don't underestimate the power of scene groups. Just because the code has to be signed doesn't mean it can't be altered. Generally a signed code means the only launch executable and often times things can be tinkered with at the hex editiing level and still left intact enough to run, so updates could be potentially stripped if the new games aren't dependant on the firmware updates for new features. They have said the cart has some upgradeablility which means it has to flashable or it would have zero upgradeablility.
Also Nintendo is not nearly as aggresive at doing firmware updates as say Sony on PS3 and Vita. Generally a new Nintendo FW comes out, they block the flash carts, within days the cart is unblocked and then Nintendo just waits to do another update until they are ready. I don't forsee a different pattern as Firmware updates are annoying, run the small chance of breaking your hardware, and this 1st generation cart is going to be lucky to sell in the hundreads of thousands (really lucky) on an installed userbase of 30+ Million.
It seems they are beating around the bush whenever someone asks about the save issue. I don't have high hopes for this.
I know that is my biggest concern as well. Look we know it has eeprom on the catridge so if it comes down to using an R4 type device to save and restore backups that will be a pain but similiar tactics were used on the early GB/GBA/DS flash carts so you know it sort of comes with the territory. The key here is the cartridge slot has been hacked/cracked and you can bet other more experienced/reputable teams like R4 and Supercard will have products out in the coming months. I can envision ways to deploy multiple roms and multiple saves without truly cracking the 3DS wide open.
How about this.....SuperCard makes a dual DS/3DS card with a switch. So you flip the switch to go into DS mode and then they make a DS app that lets you switch 3DS roms and do eprom saves as restores to flash .sav files from the DS mode. Then you pop cart out, flip switch and back to 3DS mode. I see no reason why this wouldn't be possible with a little engineering. No way this will be the end of 3DS flash carts, this is only the beginning.
Also I think thru hardware it would be totally possible to mirror the eeprom to the SD everytime a write to the eeprom occurs. Then anytime the catridge is re-powered you just flush the eeprom and populate it from the flash file.....maybe gateway won't be this advanced but someone else will work it out if they don't
I know I am sort of flush compared to a lot of people but to me something that I can play around with the current library for $80 is pretty cheap. I already have a dozen or so 3DS games and just want something to try out the obsucre titles I likely wouldn't buy or haven't found at retail. The 3DS is not really much of an 'online' device for me so if I have to keep it at current firmware and offline for a while that would be fine as I have plenty of content to work thru inluding Lugi, DKCR, FE, and Prof Layton which I have purchased in recent months and haven't gotten to. Still trying to finish Kingdom Hearts so between the games I have and stuff I will mess around with on this cart it could be 4-6 months before I upgrade and by then other carts will be out or gateway will be updated. I have tablets, phones, laptops to do my social networking, browsing, and Consoles to play online.....the only thing I would miss are some eshop titles but again I wouldn't be offline forever....I guess its a trade off anytime you embrace 'mod' equipment and in some cases I will own two consoles/devices to have one OFW and one CFW....again I am older and have more resources than many so I understand not everyone can do this but in that case you just have to pick your poison!