We all have different opinions on what is fun and what isn't. I think of JtP and the (previous) anachronism missions as my absolute favorite.
Mission choice is like pizza toppings. No way everyone
will agree. If missions keep being changed for the people who won't
play them, the people who liked them before will lose out.
Everyone should vote up this issue
on mantis. It is about a server configurable list of each mission type. They could be toggled on and off, changing what types are available for seeding in the world. There could be all sorts of limitations added in, if needed for balance, but I think it's the only way.
Missions could be added on a trial basis even. The devs could add it in with a default to "off" and those who want to try it out can. There could be different versions of missions that are mutually exclusive. This will certainly stop people from being "ticked off" when they get a mission type they hate, and the perfect response to those who do complain and think the whole
game is ruined because of one mission type.
Those missions people don't like tend to stack up. 1/3 of all missions are going to be the ones not liked, since they will stay around the longest.
Space Rangers 2 had a whole bunch of distinct game types in it, Text Adventures, RTS, arcade, etc. It let you turn off aspects of the game you didn't want to deal with. It worked quite nicely.