You forgot the part where third parties talk about how smart Mulder is while he almost never demonstrates it on-the-ground and constantly gets things very wrong while being used by not-so-invisible puppeteers.
I think getting old is when you realize that Mulder is completely irrational, his instincts are wrong 99% of the time, and he's kind of a dick sometimes. Often. He's so over-invested in his own personal drama that he misses almost everything that happens around him.
In comparison, Scully is super open minded, if you show her an alien she'll be like "yup that's an alien" and immediately start studying xeno-biology. Despite Mulder's horrible track record she'll often give his outlandish ideas the benefit of the doubt and try to bear with him.
Mulder doesn't need to act smart or even be smart. He's right. Scully is over here earning an Olympic gold medal in mental gymnastics trying to explain the absolutely supernatural/alien shit as something mundane just because they found one conspiracy led by humans making shit appear supernatural.