DrFranknfurter, Ion Cannons already paralyze/disable ships. If the only targets left on a planet are too high mark to insta-kill, the cannon will still shoot it, reduce it's engines to zero decently quickly and then paralyze it with each shot afterwards. I often have some MKIV&MKV ships stuck at random AI planets for literally hours because a wimpy low-level Ion Cannon is shooting them (and they can only move a few centimeters inbetween each shot, meaning it takes them forever to reach a wormhole, get out, and start going home), which is pretty hilarious.
Onto the "Ion Cannons not worth it" thing (and keith's suggestion which I actually think would be fun):
I agree that currently Ion Cannons are not worth it, low level ones are too bad to build, high level ones are near-impossible to pay for, and you generally ignore any MKIII or lower ones you capture (and when do you ever get lucky enough to have a MKIV/MKV Ion Cannon randomly placed in a system you want to capture and use as a choke point?).
But isn't this issue simply solvable by "OPTIONS! OPTIONS! OPTIONS!"?
Just like the WarpRelay<->CounterPost problem we have had recently (where I'll pick Warp Relays ANY day of the week), you could just let the player choose between a variation of ion cannons in the lobby (with the exception that, unlike WarpRelays and CounterPosts, "neither" and "both" are not an option).
One variation seeds Ion Cannons onto AI worlds (and the trader inventory) as they are now, the other seeds modified Ion Cannons which always kill all marks but just have varying attackspeed (or number of projectiles, or both) depending on their mark.
Also, the "Planetary Maw" option DrFranknfurter suggested sounds amazing (5 marks like ion cannon, higher marks of it -> higher rate of eating and bigger "storage"), I'd like to go up against that (and capture it / buy it from a Trader) kind of superweapon.
Hell, there could even be yet another variation of that which spits out the ships as reclaimed zombies (or just normal reclaimed ones) after having digested them to death.
Ignore the following part please, you'll save yourself one facepalm...
And now that we're on the topic of Ion stuff and balance:
Spirecraft Ion Blasters are pretty pathetic right now. Only 4 targets per shot are not really enough to noticeably impact a battle (early game you have little access to asteroids and few resources and enemies aren't numerous anyway and lategame small fleet ships, even MKV ones, are not big enough of a deal to care whether or not 4 of them get insta-killed every 4 seconds) and the Ion Blasters' health is pitifully low considering they're only mid-range fighters (MKII flagship is tougher than an MKV ion blaster).
I get that being low-range is their specialty compared to "standard" Ion Cannons, but they're just not in a useable state. They should either be made into a lot more powerful combatants (a lot more survivability and more targets per shot) or a lot more numerous (quadruple cap and give us 4 built at once out of each asteroid while reducing their attack speed a bit maybe?).
...
God damn it I'm getting old and forgetting stuff I read (and was happy about) mere days before.