So, after playing quite a few Epic games against the Transport, the Tantive, and both at once, I've come to the conclusion that while Ion weapons are great against both:
Ion Pulse Missiles, while only being a one shot trick, are more effective.
Ion Pulse Missiles are much more effective against the CR-90.
The reason for this seems to be the weaponry. While the Transport may be hard pressed to spend off all its energy in one turn unless its pilot is making liberal use of the Recover action, the CR-90 depletes its stores almost every turn. That being the case, it's much more likely that losing out on 2 (or even 4) energy in a single turn can completely shut it down for that turn. Assuming that the person flying it put decent points into the thing, that could be between 120 and 150 points that are completely shut down during the combat rounds. The last game I played, that single turn of not firing cost the CR its life in only 3 combat rounds (and not even needing to really focus fire on it that third round, half my squad got to shoot at other targets). Thanks to the rather large blindspots in it's range and arc, that main Turbolaser turret just isn't enough even with 4 attack dice, because most imperial ships are getting a minimum of 4 evade dice against it. Without absurd luck (or spending more energy), that turret just doesn't get the job done enough to make up for losing those secondary weapons.