We are definitely going to want to make sure the next version (which WILL be the standard version) is compatible with the latest File Replacement (or whatever Phantom Wings is calling it now) code, but at this time we're not very sure about it in general. Hopefully more detailed information will be developed about the nuances of its code interaction so everything can work out.
By the way, integrating throw mods into this is proving a pretty awesome endeavor. Glitchy looking throws on Falco, King Dedede, and Pikachu are gone, in general CGs are much more fair where they remain (Bowser players rejoice), and it may be just what a certain Captain was always looking for. As of right now, our project is finally bringing ICs up to the design standard the rest of this project holds...
The list of throw changes we have planned isn't particularly short right now; look forward to it. A preview of an example is that we are going to make Kirby's Copy do 10% (same damage as spitting them out) and be safe on hit so, unless you actually are getting a positional advantage from spitting them out, there's no disadvantage to taking a power. It also means we can finally buff Egg Lay, though admittedly it's only a slight buff we can give it (more damage)...
Sir Orion, do you have the gameconfig.txt file in the root of the SD card, and are you using Gecko 1.9.1? Using an old version of gecko or missing the gameconfig.txt file are the two most common causes of that issue.