Browsing through Pocketheaven forums i noticed this post by DCEmu Member/Coder Ingramb:
If a new version comes out, it will use a folder rather than the root. Never got around to doing this. If someone wants to release an unofficial version with this enabled, that's fine with me.
Frame skip wont help too much, because as JLSoft says, video rendering is fast. Loading data from the card is slow. Emulating the CPU is slow. These things are harder to skip unfortunately.
When is a new version coming out? Not really working on NeoDS for now. There are other projects I am interested in. I would like to return at some point, but there is only so much time. We'll see. In the meantime, the source is out there. If anyone wants to release versions that adds some commonly requested features like loading roms from a different folder, that's cool. I'm even willing to offer some help, either through this board or via email.