Gateway actually stores the .sav files on the System SD card instead of the Gateway SD card. Card 2 games alter the .3ds file on the Gateway card, though. (The "Last Modified" value does not change, but it can be verified with an MD5 checker, or any other method of comparison before and after.) I don't know if they chose to do it that way because of fragmentation issues, or if the way their Home Menu hook works prevents them from accessing anything other than the currently loaded rom/save data and the System SD card, or if there's another reason.I see. Well you won't lose save data from updating. You can use use a program such as savedatafiler (google it as I can't link to this I think) to backup and restore your saves. You can also use the emunand tool to backup your emunand as a precaution before updating it. This would make it impossible to lose your saves (note that if you are running games directly off the gateway micro sd, they will be stored on the gateway micro sd, and emunand tool will not back this up. Emunand tool will only back up whatever is in the emunand partition on your internal sd card inside the 3ds - such as eshop game (CIA) save files).
GW - Running games straight off the gateway micro sd, the saves are stored on the gateway micro sd. Note they are not actually written to it until you exit the game.
Sky3DS - What I can gather from this manual, is that the sky3ds stores saves on the sky3ds micro sd.
CIAs - The saves are stored in the sd card inside the 3ds.
It is easier to use Gateway for roms you can't get in CIA form. The save files can be read directly in windows explorer (they are *.sav files). Sky seems to store them in an encrypted format for which you need to use a certain program to access them. From what I have read quickly, it may be possible to convert the saves to Gateway format depending on the game. This thread has some information. I didn't find any information about Gateway to Sky, but I'd be surprised if someone hasn't figured out a way to do it.
I've had the battery die a few times on me, and I believe I've recovered the save each time. If you load the same game that was previously loaded, Gateway won't overwrite the save memory. Then you can start the game and close it, to have it write the file to the SD card. I'm not sure what will cause this to break (like taking out the card, leaving the system completely drained for too long, etc), so for best results, I would recommend doing this as quickly as possible.Ah I did not know you had to close the game to write the saves for the gateway, might be a bit of a pain if the battery dies I'll have to test if this is the same case with Sky. It is a shame they aren't easily convertible from the looks of things. I did notice a few times when I tried to get the OOT save exploit working that Sky would just delete the save, it seems a bit fickle.
I think, like you say, in the end gateway is the best of the two cards although it is more complicated to set up. I like the Sky as it is easy to use, but I feel gateway will always be that bit ahead (being able to play CIA is also very good as some titles are only available via e-shop).
I'm happy with both cards as the Sky enables me to use the gateway If another exploit is found in another game then I can just stick it on the Sky, easy.