Right, you cannot run GBC games natively without a dedicated GBC flash cart, which would be very difficult to find nowadays (not to mention expensive as heck).
Try the latest WIP build of Goomba Color, which has better graphical accuracy. Instructions:
1. Grab the Alpha 6 download from
http://www.pocketheaven.com/boards/viewtopic.php?t=3280 (this is the one the Supercard SD uses, but includes the builder tools as well).
2. Replace the goomba.gba file in there with the updated WIP build from
http://www.dwedit.org/dwedit_board/viewtopic.php?pid=1740
3. Follow the instructions at
http://wiki.pocketheaven.com/Goomba to create a compilation.
4. Patch it with the Supercard patcher (otherwise it will come up blank when you try to run it). Use whatever patching options you want, though I personally use as few as possible.
No clue if it will help with Shantae, but it helps dramatically for GB Donkey Kong games.