Is using prefix really all that annoying? I run Ubuntu as well as OS X, and I like to keep my compiled software segregated from my package installed software. This means I "prefix everything". I mean really, using --prefix is minor in contrast to some of the other difficulties encountered when compiling software.
Homebrew has advanced the state of package management on OS X significantly. Anyone considering a Mac laptop should look in to it to see if the packages you need are there.
http://mxcl.github.com/homebrew/