You don't have to submit it to Bis's site (which is primarily focused on "perfect" game runs).
You could submit it to SDA, for instance. Just plan out an ideal path that allows for stopping in a handful of save spots... and then just run from save spot to save spot (recording each attempt)... and then select the best trips between each spot.
this method will naturally result in slower runs than are actually possible... but it's like using long-term save states.
if you could do both castles in c:sotn in 10 saves, i'd be more impressed than someone using vba and not needing to stop at one.
Here's a question for ya, Bis: Would you consider posting an AVI without an accompanying keypress file (fmv, etc)?
For instance, VBA can record directly to AVI. This includes savestate loads, which means that minor video editing could produce a "seamless" GBA game run, by cropping out the reloaded parts of the AVI. The only problem lies in the lack of a VMV, since it doesn't support savestate reloading within movies.