Increasing the limit by a small number would be very nice. There is no good way to decrease the number of files since RPG Maker MV simply generates a lot of files. Specifically, there are already less than 500 files in the project, however, the folders are also counted as files.
Viewing post in Maximum number of 500 files for HTML5 games
For an HTML5 game, it should be able to load within a certain amount of time (even on slow connections). This isn't NewGrounds where every game has a several-minute loading bar (or longer).
If folders are being counted as 'files' then that may be a bug in the system. However for now it may be useful to offer a downloadable option in the interim.
I feel that instead of a 'number of files' limit that itchio just have a 'file size' limit for HTML5 games and devs offer a download option for larger projects.