Is there a way to increase the maximum files i can upload for my html5 game to 2000 files? If so, how will it affect the user experience?

This feels similar to the "contact us if you need more space" thing.  So try using this link.

For anyone that stumbles on this topic, send a message to http://itch.io/support to request increased limits on your account.

For this particular topic, 2000 files is way too many, and we probably won't approve it. Try to find a way to make your game use less files, since more files generally means a worse user experience. If you need a lot of files then consider a downloadable game.

I also need this limit raised please, most of my files are sound effects in a large adventure game, I don't think having over 500 files is a surprising thing these days in a decent game, especially the way html5 deals with sound files. The game itself is only ~39meg. I will get it as close to 500 files as possible though.

Cheers.