Frequently, when actually needing to compile other things (outside of macports), Macports would be pulled in "magically" and cause issues (such as gettext and Python-core). Frequent issues debugging strange issues when trying to port install things, etc.
Homebrew does just enough to work, and get the job done and attempts to "fit in" with the OS I already have, versus making it's own sandbox off to the side.
The problem with accidentally pulling in libraries seems unavoidable with Homebrew since it uses /usr/local. Is the lack of sandboxing what you think makes it better? This seems like exactly what you should be looking for.
While I agree that it would be nice to have seamless integration with the OS, having a completely separate installation helps with things like OS upgrades or when you need to use a different version of a library that is installed by the OS. Does Homebrew do anything to handle that kind of problem?
It can use /usr/local - and you can set it up so that /usr/local comes before the rest of your system as you need to. Yes, an entirely self-contained sandbox avoids this, but most of the time, I don't want that.
Like I said in a previous comment, most of the time I'd find myself compiling things by hand into /usr/local anyway.
Please! Use the system's provided libraries. If I need something newer, I'll brew install it myself. For me homebrew strikes a good balance between "compile it myself, damn it" and Macports/Fink. The formula are easy to hack and update (it's simple), and for the most part it just gets ourt of your way.
