Gateway can do that; You'll use the blue card to run DS games through the sysnand, and the red card to run .3ds roms on emunand. You can also install .cia to gw emunand.
By having your sysnand on 9.0-9.2, you won't need the DS profile exploit to easily launch gateway mode (you can set menuhax + ctrbootmanager). For playing 3ds games you would just boot into gateway mode (on emunand) and run either games installed as .cia or .3ds roms through your gateway red card. For playing DS roms, you'd boot into sysnand with the blue card inserted and launching the labyrinth game (which leads to the rom selection menu). Note that for using the blue card, you'd need to install bluecardfix.cia into your sysnand, which can be done by using rxtools pasta + fbi.