It's not even like the idea of objectives is that bad. I enjoyed the missions in SH4, particulary dropping people off or rescuing downed pilots. Like Elanaiba says it's maybe as much to do with presentation as anything else.
Personally, I never liked the idea of the renown system - it always seemed a cheesy way of saying 'score' to me. But what if special missions and so forth were tied to renown? If you are a famous enough skipper you might be picked by Bdu to enter a Harbour and sink a specific target,( Yeah, just like Prien,) It makes these special missions something different and special and makes working towards being trusted enough by Doenitz something important. Tie in access to new boats in the same way. In the campaign expansion for 43-45 (

) imagine being called into the flotilla office one day as a Renowned skipper and asked whether you would like to take command of a new type XXI...That would add something, would it not?
I think this would allow the best of both worlds - access to sensible and historically plausible special mission that may lead to tangible bonuses (Medals, promotion etc, ) and give a deeper 'gameplay' meaning to you long and dangerous patrols.
FWIW, I don't like missions in a sim of the 'sink x number of battleships' type regardless of whether they are optional or not. They don't feel right and spoil the immersion. But if the game had something like I outlined above I'd be very interested.