The best I can reasonably think of is having a WAD processor built in for EZ Flash Omega, so SD card WADs can be loaded into the ROM bank with the game code (essentially modifying ROM) in a GBA friendly format (as long as that format doesn't make the ROM consume more than 32MB.) and otherwise fall back to a pre-processed WADs that are already in ROM via GBFS or NitroFS.

The cool thing I did was make WADs load from SD card on EZ Flash Omega, so Doom WADs could be loaded from disk: there definitely isn't enough memory to do that sensibly - with the EZ Flash Omega you can bank the ROM address to a difference section of the flash cart's PSRAM (or whatever) so you can load a WAD from SD into PSRAM and bank in/out of it whenever you need to read it (treating it as 32MB of RAM banks), however that requires a good chunk of code to sit in IWRAM just for banking during read/writes and that's space that could be used for accelerating the 3D renderer, which always consumes the most CPU time.

I had gotten Doom WADs directly loading in GBA before, but realised my code sucked before I got as far as auto-map (hence why I started re-tooling, and then later thinking 'I should do Wolf first'). I had imagined I may need to write a WAD processor like you have. I think I can get Wolf3D running very fast on GBA with BSP rendering, it's just so much more efficient than ray-casting (such a big CPU drain). Yes the plan of first doing Wolf3D came about from my disappointment at the official port. Gave DIY Doom a quick read, I'm now tempted to skip Wolf3D and go straight into Doom.

Doom 2 gameboy advance