You can write standalone GBA homebrew, can even probably do it all in C (though some inline assembly might help) -- plenty of really nice long form games exist there, and would still fit with the "runs on GBA hardware" thing if that is somehow a thing you want to do. https://devkitpro.org/ being where most would start with that today for that one.
As it stands I am no great artist, not much of a UI designer, would call myself a ROM hacker, know ARM assembly, a mediocre C coder at best and the GBA is very much in my wheelhouse. I would still pick homebrew from the ground up for making a fan game over hacking a ROM as a basis for a whole new game.
Honestly because I thought hacking an already existing ROM would be easier I hadn't considered this way of going about things. Based on what you're saying though it sounds like building the ROM from scratch would probably be my best bet, so long as I can still achieve the same results of course. It's very unlikely I'd be able to manage this alone however (at least without many many years of experience) so I may opt to higher a professional instead. I know this may be hard to answer but do you have any idea what the price tag for such a project might look like? I'm sure it's going to be pretty high up there but exactly how high I'm unsure of.