What a coincidence. I was just talking about missions in another post. I don't mind alternate missions per se, but I agree they occur far too often. I'd like them to "shake things up a bit", like giving the option to refuse an alternate mission when offered, which would lead to the ship making the offer turning on you. Or, if you accept the offer, but then renege, have the other faction try to interdict you in the next system you jump to. Also, maybe have some alternates turning up only at the time you make delivery, when you go into the bulletin board.
I also mentioned in my other post how I'd love to see them bring in more non-linear missions in future. Maybe that could apply to alternative missions as well.