One thing that always bothered me with RTS is how it crashes the game if you do it many times. Also some games can't do RTS until you load the respective save file. (looking at you, Harvest Moon and Final Fantasy!) It's safer to ...just stay away from RTS.
Yeah, these are pretty much the things I used to have trouble with as well. Most DS games allow you to save at pretty much any time anyway (except that spooky RPG where you are a witch and encounted monsters every five seconds, and the battles are on average literally half an hour long).