On the off-chance that you're as confused as I am, the Baltimore Sun has a fairly illuminating interview with Anthony Cordesman about the violence that's unfolding in southern Iraq:
Much of the current coverage of the fighting in the south assumes that Muqtada al-Sadr and the Sadr militia are the "spoilers," or bad guys, and that the government forces are the legitimate side and bringing order. This can be a dangerous oversimplification. There is no question that many elements of the JAM [i.e., Sadr's Mahdi Army] have been guilty of sectarian cleansing, and that the Sadr movement in general is hostile to the US and is seeking to enhance Muqtada al-Sadr's political power. There is also no doubt that the extreme rogue elements in the JAM have continued acts of violence in spite of the ceasefire, and that some have ties to Iran. No one should romanticize the Sadr movement, understate the risks it presents, or ignore the actions of the extreme elements of the JAM.
But no one should romanticize Maliki, Al Dawa, or the Hakim faction/ISCI. The current fighting is as much a power struggle for control of the south, and the Shi'ite parts of Baghdad and the rest of the country, as an effort to establish central government authority and legitimate rule.
The nature of this power struggle was all too clear during a recent visit to Iraq. ISCI had de facto control over the Shi'ite governorates in the south, and was steadily expanding its influence and sometimes control over the Iraqi police. It was clearly positioning itself for power struggle with Sadr and for any elections to come. It also was positioning itself to support Hakim's call for a nine governorate Shi'ite federation -- a call that it had clear Iranian support.
The US teams we talked to also made it clear that these appointments by the central government had no real popular base. If local and provincial elections were held with open lists, it was likely that ISCI and Dawa would lose most elections because they are seen as having failed to bring development and government services. ...
This does not mean that the central government should not reassert control of Basra. It is not peaceful, it is a significant prize as a port and the key to Iraq's oil exports, and gang rule is no substitute for legitimate government. But it is far from clear that what is happening is now directed at serving the nation's interest versus that of ISCI and Al Dawa in the power struggle to come. It is equally far from clear that the transfer of security responsibility to Iraqi forces in the south is not being used by Maliki, Al Dawa, and ISCI to cement control over the Shi'ite regions at Sadr's expense and at the expense of any potential local political leaders and movements.
The whole thing's worth reading, and it sure sounds like the sort of complicated sectarian feud the United States isn't terribly good at refereeing (according to this counterinsurgency blog, many U.S. officials have preferred to side with ISCI simply because they have people who speak English). Iran, meanwhile, appears to be supporting all sides in Basra, to end up a winner no matter who comes out on top, although Marc Lynch flags a rival theory floating around the Arabic press: The Iranians no longer find Sadr useful (they've got all the proxies they need) and are cutting him loose.
For his part, Phil Carter argues that Maliki is "using the Iraqi security forces to consolidate his own power and eliminate his rivals," adding that the Sunnis who have so far been cooperating with the United States must be watching this operation with a fair bit of dread. He goes on: "Every time you think of the 'adviser model' for Iraq, you should think of this operation in Basra. Because this is the end result of the U.S. advisory effort to date—which has focused on creating well-trained and equipped units at the tactical level, but has basically failed at the national, strategic level. The leaders of the Iraqi security forces at the ministry level are as bad as they ever were. And the national government is about as bad. Training and advising Iraqi units at the brigade level and below is well and good. But if you fail to properly shape the national command structure, you're handing those units over to leaders who will misuse them."