One thing to remember about Morrowind is that it's not safe to take everything at face value. The Mages, for instance, will give you quests varying between "trivial" and "borderline suicidal for a beginning character", and there's no good indication of which category it falls into until you try it.

It is possible to make both the Fighters' and Thieves' guilds happy, but you need to be careful about it. They are engaged in an ongoing feud, which you can defuse if you handle it right, but if you just blunder along doing what you're told, you'll just walk straight into it. I think the fighters are the most troublesome faction in the sense that they are most likely to get you into trouble with other factions.

And there's the Camonna Tong, who fulfil about the same role as Skyrim's Thalmor - existing solely to be cartoonishly evil.