Epic's never said that UT2003 mods would work with UT2004 without edits (see Loibish/Wong). Jeebus, Edo - YOU KNOW THAT. You know that every patch of UT2003 alone can easily break a mod's compatibility causing the team/coder to have to update. That's been true since ... modding began. If you dislike it so much, go mod for the Half-Life engine, where Valve where break things in your mod just to get it to work for Counter-Strike.
This is nothing big, or different, or horrible for mods. It's better code and better performance, and my only complaint is that I don't get to play with it for another month or so.
(also, every other engine out there to mod is undocumented as well)