To be clear, most of it is reasonably common sense for a character that can show up in any random group, with any random GM, for one adventure at a time:
- You can't use books that only just came out on PDF, because not enough people have them and know them
- Some of the weirder things are not an option
- negative qualities that are more story oriented or which require games to be built around them more are not allowed
- there are a few balance things, and some 'this rule is ambiguous: here is how it will be interpreted for Missions" things.
So there is things to pay attention to when making a character, but I know that if you happen to use Chummer it has an option to only show things that are Missions legal (it may not be perfect, but it should get you at least really close). I find that helps when I'm looking at Negative Qualities, to only see the ones I can choose from.