No trouble at all with the DSTT. It is my favorite. It uses standard cheats and saves. I do not want anything that doesn't!
I can boot to TTMENU and switch to YSMENU and back to TTMENU without reseting power!
I have two NDS loaders, 2 .gb emulators (LameBoy and Goomba) and 2 .nes emus (nesDS and pocketnes).
I also use NO$GBA for .nds files and VBA for .GBA and .gb files on my PC.
I have used Rudy's backup tool to recover .sav files from retail carts.
I have used POKESAV and Thundaga to edit .sav files.
MOST of the sav files can be moved between TF card, save editor and emus without problem - even if the file size changes.
DSTT .sav files are compatible with those of R4 and SOME other carts (some require a name change).
BUT I have found a couple of serious problems with save files on emus:
1. A 512kb .sav file from NDS works fine in NO$GBA, but NO$GBA shortens the .sav file.
That shortened .sav file will not work anywhere else I have tried.
2. An 8kb .sav file from made by LameBoy will be killed and replaced by a new 64KB .sav file by Goomba.
That's it.