Has anyone

[ZiNgA BuRgA]

Most other systems which don't use hooking have some sort of automated code editing solution, which seems fine to me as end users still don't need to manually edit code.
It's perhaps a bit less secure, though I don't think it's that big of an issue (in MyBB, inc/settings.php needs to be writable, for example).

The code editing system will often be a lot more flexible than hooking.  I find I spend a lot of time trying to come up with clever workarounds to the hook system, since the number of hooks is limited.