I'm all for a more profits oriented approach on both accounts. If there is going to be a Robin Hood-esque questline, make it a separate faction. Or not so much a faction, but a couple of dudes with a cause. You could even have them associated with the Thieves Guild. They could be in the employ of the Guild and decide to do a little good on the side. But they aren't just gonna come up and ask you if you want in, conditions would have to be met for them to trust you. Because missions on the side are dangerous, the Guild higher-ups might frown on it. It could be a point of contention in the Thieves Guild quest line, but it shouldn't be the focus.
Similarly, certain elements of the Dark Brotherhood could worship Sithis, people got beliefs, but it shouldn't be the standard belief system of the faction. It could be another aspect of internal struggle. Believers could approach you, "Have you heard of the teachings of Sithis?"
Basically just more internal and external faction conflict, period.
What they should have done was to set it up like the Barksdale organization in The Wire...
Yes.
Everything should be more like The Wire.