Agree this is a huge problem. It's not just the Scc attributes. The mere fact that projects within the file are numbered in order means that the slightest change will cause a huge ripple effect (depending on how low its # is). Predictability is also an issue; as soon as you add/remove something, you never know when VS will decide to re-number other unrelated projects just for fun. Finally, the lack of a standardized, user-verifiable structure means that editing by hand is fraught with error.
Frederic, here are some existing Connect bugs:
https://connect.microsoft.com/VisualStudio/feedback/ViewFeedback.aspx?FeedbackID=106331
Please add your vote. MS does take them into account.