Estimates are broken. We've just fixed them for you
aboutfiveminutes.com
aboutfiveminutes.com
http://scribblethink.org/Work/kcsest.pdf http://scribblethink.org/Work/Softestim/softestim.html
It's hard to outwit Goedel and Tarski on this stuff.
Obviously, there won't be a strictly mathematical solution. Neither optimal one. We can try to create something that is good enough for a limited set of problems, though. If it works at least in half cases, then I'm happy.
I don't think we can create a methodology or magic something. But having a repository of estimates for similar projects could be great.