I can imagine a handful of reasons why PARI was left alone (if it was to be chosen *now*; can't say about "back then").
1. MPC is a GNU project.
2. MPC is LGPL3+, PARI is GPL2 (but even that it conveys in an ambiguous fashion).
3. PARI is not autotoolized.
4. PARI's coding style is not GNU (important for the GNU style police!)
5. Something that I have noticed as a distro-level packager: Scientific software often is subpar in code quality, like breaking strict-aliasing and whatnot.