The most obvious answer is that it was a last minute decision to change the Aero theme. They were doing minor tweaks to the theme the previews and had touted a feature to have auto-color for Aero Glass originally. That changed all of a sudden right before the RP came out and suddenly we hear about a new theme to flatten the OS.
The auto-color feature is still there. I also think they did not plan to replace Aero with the new theme until the RP came out. I think it was a wise choice. As nice as the RP theme looked, it really didn't fit the new start screen at all. While the desktop still doesn't match 100% with the start screen, at least it fits much better than Aero.