Don't forget that both MPC and MPFR are required to build GCC these days, for constant expression evaluation and for loop optimization (http://gcc.gnu.org/wiki/Graphite-4.8). So, MPC and MPFR are used individually and as dependencies for other modules.
Maybe part of the reason not to use Pari/GP is because it's not organized in a fashion that makes it suitable for all of these different uses.
Also, maybe there's no reason at all. Perhaps it just ended up that one developer used MPC for something, which got used by somebody else, etc. IOW, path dependency.