Do you want story-missions that are profession specific or not?
Both definately.
Do you want side-defined missions, or missions for everyone?
Sided!
Do you want the quests to scale with your level? (So you may take the same mission at lvl 30 and at 100, only with tougher opponents?)
Yes
Do you want many small, or fewer longer quests?
Again both. For the sense that small quests can give you that sense of accomplishment and that the longer quests can be fun to complete over time and give you something to look forward to everynite.
Is it ok with you to camp spawns, like we see in other MMORPGs?
NO, NO, NO!
Is it ok with you if we interweave the normal auto-content mission system in this, so that we can generate areas for you even in these story missions? (Or do you want only outdoor action?)
Most definately ok to interweave with mission system.