At this point, my main reason is "Gentoo sucks less"
The second reason being, "I know it"
:-/
A good OS has yet to be developed. Gentoo is probably less of a PITA than most, especially if you have a reasonably fast machine to run it on.
I do wish stuff like installing a printer, printing over the network, etc was easier; I believe that the OS should make _some_ decisions for you, and these should be made by the most qualified people.
I also think Portage should be a bit more automated and smarter. For example, if I do "emerge [a nonexistant package]" it goes and calculates dependencies, instead of just telling me "there is no package X". If I make a typo, or can't remember a package's name exactly, this can freak me out. I cannot use the search function because it is ridiculously slow. I know there exist external programs for this, but it should please go into portage already... please...
Also, unneeded dependencies (orphans) and double packages should just be cleaned out already, automatically. Old distfiles should also be automatically cleaned. I know there are valid points to be made against those, but can this please be the default, and let advanced users switch the automation off, instead of requiring manual cleanup by the casual user.
And let's not start about "X config files need to be updated". I like to ignore that message as long as possible.

Subversion can keep track of single-line changes in text files; why can't portage? The fact that it even asks me if I want to substitute a blank config for my painfully hand-tuned one, is insulting. Why are there even 100 config files?!
Portage is probably my main beef with Gentoo, which is a bit sad. At the same time, it is the reason I prefer Gentoo to FreeBSD; along with framebuffer, 3D support, and the Linux kernel.
My other problems with computers in general aren't affecting gentoo, though. Examples: The development "structure" and "goals" of wine, and the arrogance and stubbornness of its developers, who seem to be turning it into ersatz-Windows. The default advice is "open regedit and do X" more and more often. Excuse me, if I want that, I can just install Windows 98. I sadly need wine because I make Quake levels, and some tools are Windows only; on the other hand, a benefit of wine is that some things run faster than on Linux. Another problem is the fact that there is simply no good browser. It seems impossible to make one :-/ Same goes for graphics software (Gimp is ridiculously slow compared to primitive Windows programs running in Wine), audio software (running Goldwave in wine is superfast compared to something like Sweep), etc. pp.
That has nothing to do with Gentoo, though. More with Linux or even OSes as a whole. I just generally wonder why Windows programs running in wine are faster, and why there is simply no good basic browser after all this time. I use opera instead of firefox or konqueror, even though all my other stuff is GTK, and opera isn't open source; I use goldwave instead of audacity, even though it requires wine and isn't open source; I use stuff like Wally, and probably soon PSP, instead of gimp because gimp is so bloated.
It's about finding the least painful alternative, a lot of the time. This means that my setup is suboptimal, most of the time.
What good are CFLAGS if opera or [$windows_program in wine] are just faster, slimmer, neater? ^^ Do I need CFLAGS for vim, mutt and irssi? I think not. I use almost no open source apps for browsing, graphics, sound, modelling (don't suggest Blender plz), and word processing (I have abiword installed, but am seriously considering Textmaker).
I am becoming suspicious of open source projects when there are too many people involved. I believe many cooks are detrimental to the quality of the food :-/ I'll take a shareware program by a small, determined company over something like Gimp, Firefox, Openoffice, or KDE anytime.
The part I love most about Linux (you may insert /Unix here) are, frankly, command-line programs. I wouldn't want to give up stuff like vim, mutt, irssi, gcc/make, fbi, even elinks, and specialized command line stuff like sndfile-resample, sox, normalize, mpd/mpc, and so forth. For graphical applications, I find myself often preferring slim commercial/closed source/shareware stuff, often older versions that have lighter hardware requirements, along the lines of Textmaker, Opera, Goldwave, Cooledit, older PSP versions, and similar. A lot of GNU stuff seems terribly bloated and slow. And when you're working with sound, graphics, 3D models etc. a lot, and have a project repository and TRAC (ticket system), of which at least the latter is accessed via browser, you WILL notice what is slow, and what isn't.
I haven't seen an OS that made me say, "yes, this is it". As long as that is so, I'll use Gentoo. I admire the sleekness of a Unix server/router/firewall, too.
Windows 98 isn't bad, though. Behind the above mentioned Unix router/firewall, preferably. But as soon as X, GTK, Mozilla and friends enter the picture, I'll pass... because that is where I start having problems with GNU/Linux.
It's like in the mutt slogan: "All mail clients suck, this one just sucks less". Same goes for OSes.