Mulder was brilliant, possibly unmatched in the Bureau, but about as stable as a sack of frogs on the point of a pyramid.
While Scully was 'just' a well above average agent she had an incredibly disciplined mind and perfect consistency in her exacting standards and work ethic.
They obviously worked better together, where Mulder's emotions were tempered by Scully's logic, but, when seperated, Scully would continue to be an excellent agent while Mulder tended to go off the rails and burn out.
Conversely, as undeniably handsome as Mulder was, Scully was ridiculously hot.