Personally, I found that the Thieves Guild (as an institution and as a quest path) was one of the few aspects of Oblivion that was better than Morrowind. The inclusion of fences was a nice touch, as was the fact that you had to steal in order to rise through the ranks. The conflict between the Guild and the Imperial Watch was an excellent part of the campaign that I particularly enjoyed. Here are a few of my thoughts on the future of the thieve's guild.
Fences.
The fences are the lifeblood of the guild, if they can't buy and sell the goods stolen by the Thieves then there's a serious problem. The questline in Oblivion kinda reflected this, however in my opinion it wasn't emphasised enough. The fences need to be more prominent in the guild's storyline. They should offer their own missions which could range from standard 'steal an item' missions to collecting intelligence, shaking down customers for payment and smuggling. There should also be more fences, perhaps 2 to 3 per city. It was stupid that if the PC stole an item in Anvil, he'd then have to take it all the way to Bruma in order to sell it to Ongar The World Weary. Perhaps it would be necessary for the PC to earn a fence's trust.
Rules.
I think that the Guild's Rules should be roughly the same ones that existed in Oblivion and Morrowind.
Questline.
Despite what I said about Fences earlier, the majority of TG quests should be given out by the Grand Master, Doyens and other Lieutenents. Missions could range from 'Steal an Item' to Prison Breaks, blackmail, smuggling, helping your fellow thieves, internal politics or conflict with the law and/or rival gangs. It will be interesting to see if the TG has to compete with another underworld organisation in Skyrim. Rank in the Guild should be awarded through the system that was in place in Oblivion. However, the PC's skills should also be a pre requisite for rising in rank. It would be stupid for someone to become Grand master with Security and Sneak skills at zero.
Prison.
When you opted for Jail in Oblivion, you actually ended up in prison, you then had the option of attempting to escape. That was pretty cool, however I think that TG gameplay 'on the inside' could be made even better by the introduction of fellow prisoners in there with you. There don't have to be many, maybe 4 or 5 in each city jail. They could offer missions, make lockpicks in return for other items and assist the PC in his/her escape if they like you enough.
Just a few of my thoughts, some of yours perhaps?