I had to deal with this upgrade not too long ago, and I've been thinking about it: it's really poorly balanced. Not in the sense that you can't beat it, but in the sense that it mucks up opponent strategy and disproportionately affects some factions more than others.
Currently, it does the most damage to units with a high rate of fire - or pretty much the entire Cybran land force. As I understand, it stuns once every five seconds and the stun lasts for two seconds. Assuming it takes a second for turrets to train on the target again, that will reduce the DPS of the mantis, brick, and rhino by 60%. Percies, on the other hand, fire once every four seconds and the EMP stun doesn't delay reload time; that means Percies can have their DPS reduced if they're caught during an odd interval, but it's also possible for their DPS to remain normal while beneath the Chrono Dampener.
Reducing an entire enemy's attack power by 60% while fundamentally removing their ability to micro is pretty ridiculous, and the "balance" is that Chrono Dampener doesn't provide a health bonus, so the Aeon ACU is susceptible to snipes if you assume it's going to be on the front line. Of course, what really happens is that both players are forced by this upgrade to play turret creep. The Aeon needs shields and defenses to make up for not having the health boost, and the enemy has to use turrets because they aren't zonked out by the EMP.
Currently, it's just kind of a broken upgrade. Overpowered in certain ways, but less versatile than personal shields, so it does nasty things to gameplay and they aren't fun things. It also works differently depending on what faction your opponent is playing, as units that are slow and have a high alpha but low RoF perform much better against this thing, or a faction capable of making combat ACUs will be able to push back against this better.
Could I propose overhauling this upgrade by increasing its effectiveness, but then moving it to the T4 stage similar to the maser and cloak upgrades? What I think might balance it out is if you make it so the stun kicks in every two seconds and lasts for two seconds. Have it impact all land units excluding sACUs, ACUs, and experimentals. Remove its ability to affect air units, since stunning air appears to be a bizarre side-effect of the ability and not a thing it passively does without exploiting its mechanics - the damn thing just needs to be more uniform in action, basically. Don't allow it to stun buildings, since that would let it disable turrets and factories by standing around them, which would just be nuts. After you do all that, increase the cost of the thing to be consistent with other T4 upgrades.
This would give the upgrade very broad defensive capabilities that apply evenly across all factions and all units, effectively nullifying the bulk of ground attacks against any position where the Aeon ACU is present. However, since it's a T4 upgrade, the other players should have access to every possible option they'd need to deal with that. At the very least, the threat of an air strike will prevent the ACU from pushing forward unless he feels he has total air control, making it a powerful defensive tool but a high risk, high reward offensive tool.
I tried reading a few threads discussing why this upgrade was buffed to this point. The core argument seemed to be "Well it's gotta affect Percies", which explains the range of 35. It's not really good practice to balance an ability by only considering a single unit, though. You've got to think of some kind of role you want this thing to play, and even with the 35 range the Percy is still the unit that fears this ability the least.