(I thought I had made a post about this before ... but may have accidentally closed out my browser before submitting it.)
Edit: It seems I just missed the old post but I have a new suggestion I think. Sorry for the double post.
I think the Ion Cannon needs some rebalancing. When I got to the dreaded Mission XIII I faced a hoard of heavily shielded units so my other defenses could have some actual effect and could make progress on culling the swarm. Then when I deployed the very expensive Ion Cannons ... I was underwhelmed.
I watched as the hoard of enemies arrived with the expectation that it would start opening the door for my Corrosive Mortars to be of some use as they, and most towers, don't seem to be very effective against shields at all. The enemies approached and the Ion Cannon fired once ... and charged ... and charged ... and fired again.
For the cost, the tower didn't seem worth it at all. I have two suggestions. The first is to shift the Ion Cannon to functioning like a continuous emitter that shifts from one thing to another as shields are worn down. This would make it useful against large groups of shielded units while also keeping it from being overpowered when used against single heavily shielded units because damage would be done continuously.
The other possibility is to give it AOE. It would doits primary shield damage to the target and the EMP effect would radiate out to surrounding units to a lesser extent. The AOE splash wouldn't be enough to compromise more heavy shielding but would be enough to take out the shields of smaller rushing units.
In either case, I suggest the DPS against shield be increased beyond the current level.