Game Maker Studio has it's quirks and limitations (as all engines do), but I honestly don't think it's the source of the problems you are having. Clickteam Fusion, which I'm using for my own project, has some really bewildering limitations in it but none of them have been a progress stopper, and I've always been able to find numerous ways to work around it. I firmly believe Game Maker Studio is the same because I've seen large, professional Metroidvania games published on Steam that play and perform very well.
I do not have your source code but I'm thinking that if you're having problems it is probably because the way it has been coded. You mention having issues with using lots of large images and sprites so it sounds like you might have difficulty with resource management, which isn't necessarily a flaw with Game Maker itself. Honestly it's something I have to deal with quite often on my own game but if you keep optimization in mind as you continue development I'm sure you'll be able to overcome these issues.