I came in with the express purpose of checking out whether "to have an agenda"to have an agenda has a negative connotation or not --– as such it was in the back of my mind. The fact that there ISis a relevant discussion here means that this idiom has in fact developed towards this connotation. As far as I'm concerned, the answer is: yes, it can have an inherent negative meaning: "John came all the way from California to see Mr. Psmith. And he had an agenda".