[Phanx]

Well, for one, putting your entire UI into one "addon" makes it annoying to maintain. You can't isolate parts to debug problems, for example. It also leads to sloppy coding, such as inter-dependencies (where something in File A depends on something in File B, but something else in File B depends on something in File A), whereas having each discrete part its own addon forces you to use scoping correctly. I believe this is one of the issues you're running into right now.

For another, it sucks for your users. Go look at most any popular "all in one" UI's comments, and you'll find people asking how they can use just the unit frames, or just the buff mod, or just some other part by itself. By shoving everything together, you're forcing users to use 500 features just to get the 5 they want. There's no good reason your unit frames should depend on your action bars, or vice versa, so you should just make each of those things their own addon, so they can be used independently. Having a central "core" that each of the other addons depends on is fine.