about the only thing I can think of that may help the factory ignition is dedicated ground lines to each coil. each coil is held down by a bolt, so, by making some ground wires, and attatching one to each coil at the hold-down bolt, you will improve the grounding path for the coils and plugs. Aluminum isn't as good a conductor as thick copper wire, so grounding each coil directly would result in a better spark, and equal intensity across alll the cylinders.
Otherwise, the factory system is practically flawless. going with a COP setup was a great move on toyota's part.
There is a company that upgrades the factory coils, but I don't think you really need it. the factory coils provide plenty of spark to begin with.
Most cars see improvement from coil, plug and wire upgrades because remote coil setups are inefficient from the get-go. putting the coil directly on each plug removes the shortcomings of poorly conducting plug wires and weak coils.