Reasons to separate:
http://www.ratbehavior.org/CommunalNesting.htm
1. Studies show females in the wild prefer separate nesting chambers.
2.If one female eats her young/doesn't nurse/etc, you know who is cannibalizing/lazy without too much investigation.
3.If the litters are not sync'd within days, the older pups decrease the survival of the younger pups. "...in mixed-age nests the younger animals must compete with older, larger animals for milk, which puts them at a disadvantage. In rats in particular, the younger animals may be unable to nurse from their own mother because the older litter has rendered her teats unusable (Sachs and Rosenblatt 1974)."
4.One mother can monopolize both litters, which decreases survival of the litters because each animal gets less milk and of poorer quality.
5. (4. cont) Females produce more milk, but not on a linear scale. "...The more young a female has to nurse, the more milk she produces. However, this increase is not linear, so in large litters each infant gets less milk per head, and the quality of the milk decreases as well. König et al. (1988)"
6. Studies show that litters raised separately are more likely to survive to weaning. "In general, captive females who raise their litters alone rear almost all of their young to weaning age (89%). Communal nesting does not enhance litter survival in captivity, and in some cases communal nesting leads to higher litter mortality (infanticide of the first litter, high mortality of the second litter)."
7. Unrelated females are less likely to share a nest. "Pairs of sisters who have grown up together are more likely to pool their offspring and to share parenting than females who have only known each other for a few weeks. Unfamiliar females tend not to pool their offspring, and when they do, one female tends to monopolize the litter. Familiar pairs of sisters are more successful than unfamiliar pairs: overall they produce more weaned offspring and are less likely to commit infanticide than unfamiliar pairs."
8. Stress plays a large role in health, stressed females are more susceptible to illness.
Obviously, people will tell you to do it. If you feel comfortable with the reasons stated above, no one is going to stop you.
I prefer to have complete control and insight into every female in my colony. This way I know when one female isn't producing large litters, what females are poor mothers, what her age is vs. production output, if I should hold females back from her line etc...