I'll answer question-by-question.
1. Do you want story-missions that are profession specific or not?
I'd love that. Not all, but some of them. Quests for a specific class are a good idea. For example, an engineer quest might involve fixing some machinery somewhere with a special tool. An agent might have to sneak into a place and retrieve documents, etc.
2. Do you want side-defined missions, or missions for everyone?
Either way.
3. 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?)
That would be nice, but not necessary so long as at the BEGINNING of the quest, it was apparent what level range was appropriate for it somehow.
4. Do you want many small, or fewer longer quests?
I prefer small, because not all of us play for endless hours at a time. If it could be completed in stages on multiple play sessions... that'd be fine.
5. Is it ok with you to camp spawns, like we see in other MMORPGs?
Absolutely not. That is one of the most horrible things in onlnie games, nobody likes having to sit around waiting for a spawn, especially when other players are all too happy to come charging in and take it from you when it finally appears. Waiting = no fun. This is a universal truth!
6. 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?)
That would be nice. I'd prefer to have the missions either indoors in a 'private' dungeon (teams allowed, of course) than somewhere camped. If outdoors, it would have to be random in the extreme to prevent people from stumbling upon something YOU were supposed to find/kill and interfereing with the mission.
An ideal personal story mission to me would pertain to your character (even if only generally) and involve you being assigned places to go which were accessible only by people doing the quest. This should not prevent OTHERS from doing the SAME quest at the same time -- which is why the personalized dungeons are a good thing. At no point should you have to wait hours (or even 15 minutes) for something to spawn.
Finally, if this is implemented well, it should involve more than going somewhere to kill someone, or going somewhere to get an item like the missions now (which I love.) Instead it should be more like.. "Get item A. Take item to someone at location B. That person asks you to go observe someone. When you come back, he nods and says, "Ah yes.. I was afraid of that. Please take this disk to his hideout at [coords] and use it on the mainframe there to sabotage their operations."
Etc.
Would be fun.
The reward items should not necessarily be incredible, but should be something you won't find anywhere BUT the mission. A different looking type of helmet.. an experimental backpack.. etc. Something useful. Best would be something you can use in addition to existing items.
A cool profession-specific mission idea might be 'training' you can go through. This would especially make sense for Omni people, but clans would have it also of course.
Training style missions would have to be something you and you ALONE are sent to do, which takes awhile to do and is a good challenge. Maybe done in segments you can complete one at a time. The end result might be a direct boost to a profession-specific skill and a change in title, or an item you can use which is unique to your profession.
How about, for the MP, a 'floating torch' replacement which looks like a tiny little glowing wisp, and while in use gives them muinor skill buffs. For fixers, a special set of gloves which enhance computer lit and look unique, etc. Engineers might get a toolbox which they could yield/summon that when held added to engineering skills. Etc. Just ideas.