I had the pleasure of doing some work Conflict Dynamics (a UN-partner NGO) on the question of Sudanese independence. My boss at the time (Gerard Hughes) was contracted to do some work on alternative models for the South Sudanese independence vote coming in 2011.
(Background: the vote was part of a peace deal ending a 30-year civil war between the predominantly black traditionalist/spiritualist south and predominantly Arab Muslim north.)
In short, there are a number of models out there that exist in a continuous spectrum between "unity state" and "two separate unity states." There are a number of "federal" style unions, including the US, Germany, Russia, UAE, Bosnia, etc, that have varying levels of legal autonomy at the state level, and (at least) unified defense and representation at the central level. The EU represents a union of a number of states, but with free transit/trade across borders, and some collectivization of resources, defense, etc. Other options exist, too. In fact, Sudan already had a semi-federal state where the South was given some legal autonomy.
Ultimately, I left Conflict Dynamics before we finished the work, but the report that came out aimed to help the UN, AU, and North/South Sudanese governments create options besides total unity and total independence. If implemented, the risk was (of course) confusion as to the details of an arrangement, which could make the referendum a disaster.
In the end, the report (and those of us that worked on it) were unable to garner political support for a more complex, nuanced relationship between North and South Sudan, and the referendum is coming, with two options: Unity and Independence (see photo). And last I checked, the measure had over 90% support amongst Southern Sudanese, who see it as an obviously better alternative than growing closer to Khartoum. Let's assume the referendum will pass.
The result is likely to be disastrous. Southern Sudan has most of Sudan's oil. Currently, a wealth-sharing mechanism is in place, but there's no plan in place for wealth-sharing after independence. Khartoum will lose a great deal of money... and Southern Sudan will be land-locked, and will likely have to pipe its oil through Northern Sudan, anyway. Piping costs will be a massive point of contention.
Three regions between Northern and Southern Sudan are in conflict (as to which side they belong). Only one is going to have a referendum on its choice for sides in 2011--the other two have no solid plans as of yet.
Northern Sudan is currently accusing Southern Sudan of supporting Darfuri rebels, and threatening war.
And, generally, there remain many displaced people (from the war) on either side of the border, and where they fall out in the census is questionable.
But ultimately, oil is going to be the big sticking point, and there's likely not a great solution for it that can be built after the referendum. I could be wrong, but the two sides are sufficiently uninterested in productive discussion, and the groups leading the mediation are sufficiently ineffective, that war may be coming. Again. Even if the disputed territories (disputed largely due to being chock-full of oil) are resolved "democratically," neither side is interested in accepting defeat and establishing a status quo out of their favor.
And, in the end, the great powers have very little interest in doing more than making enough noise to look like they're not ignoring the situation. Strategically, war would lead to a number of interesting alliances. Darfur and Southern Sudan would almost certainly combine their efforts (if the JEM is interested in independence, as well), and may even see more support from Chad and Eritria if victory looks possible. Al-Bashir, though, will shore up military support he needs before engaging in war, and may well gain support from Egypt and China, both of whom have a strong strategic interest in political stability and central power in oil-rich Sudan.
It'll be a situation worth keeping an eye on, and one that might begin chewing through one of the few tentative areas of peace in east Africa.