People often tell you that twinsets mean task loading - more to remember during a dive.
The main reason mentioned is that you have to keep swapping regs. True, the gas management skill needed to switch between regulators appropriately is rare amongst recreational divers. However, it is not neccessary when using a manifolded twinset.
A manifold is essentially a tube which connects the two cylinders together, and allows air to pass between them. By linking the cylinders in this way, you breathe from them both at the same time, and therefore do NOT have to switch from reg to reg.
The only other time that you have to do more with a twinset is when you have a freeflow. When this happens, with a pony setup, you wave your entire cylinder contents goodbye and switch to you pony. With a twinset, you isolate the cylinders, turn off the offending regulator, reopen the isolator, and still have all your air. It's more to do, true, but I'll make that sacrifice.