Thank you for your tip, I defragged the isos but there has been no changes. I also tested it on another usb-hdd with the same issues.
Here are some other tests I've done.
Super Mario Sunshine = ISO (Placed it in the wrong folder therefore not appearing and crashing on wiiflow, I guess)
Mario Kart Dash = GCIT - GcReEx
Super Monkey Ball Adventure = GCIT - DiscEx
Wario World = GCIT - DGcReEx => DiscEx
Viewtiful Joe = GCIT - DiscEx => DGcReEx
DiscEx giving the best results but it only worked every second or third time I tried to run the game.
After that test I converted all ISOs to DiscEx and I was able to start all games at least once or twice but it took up to 5 tries to get it running 1 time, without changing any settings.