One of the things I saw argued a bit when Skyrim was announced was that many(I seem to recall me being among them) wanted to see a return of skill requirements for factions, since that was how it was done in Morrowind. Looking back, however, I'm not sure having skill requirements as standard for a faction is good design.
Now, don't get me wrong, some factions would surely have skill requirements as a sensible part of it. Magic focused guilds and the Bard's College strikes me as good examples of that, since those are factions dedicated to learning and study. The whole point is, at least in principle, to get better at X skills.
However, let's look at guilds like the Dark Brotherhood, Thieves Guilds and the Fighters Guild. Those are primarily meritocracies. You're paid and advanced on your ability to complete contracts efficiently or make money. Does it actually matter if you're a mage in the Fighter's Guild? Or in the Thieves Guild? We know it doesn't in the DB, given that they are represented in both Oblivion and Skyrim. I'd say that it doesn't matter, even if it goes against the "norm" of the faction, again because these factions are meritocracies. Your formal skill with a sword or an axe shouldn't matter compared to your ability to complete contracts in this sort of faction, be it with the use of stealth, magic or straight forward combat.