The Punisher does seem to have stolen a little of the Gunboat's thunder in 2e.
Loss of LRS, reload no longer being a Gunboat only trick and the buff to Xg-1 while Os-1 gets nerfed and all ordnance now allowing you to keep and spend the TL seem to be conspiring against them. Still, FCS is cheaper than Os-1 used to be, and while they can't match the Bomber as cheap Barrage Rocket carriers, I do wonder if the extra HP, presence of shield and ability to shoot after SLAMing makes Jendon and three FCS Barrage Os-1 Gunboats worth considering. You can run two Rhos and Vynder and include Adv SLAM.
Ion Xg-1s are probably the way to go, though. Just so much cheaper to run.
One thing I do want to point out, because it's not been mentioned yet. Xg-1s don't have to attack with their ion cannon every single turn. It's not great, but they do have a primary that rolls three dice at range 1. Range 1 which, in theory, should be achievable after ion-ing their targets. That's also the same number of dice you can roll with ion and Xg-1, regardless of range.
Even if you aren't disarmed and are at range 1, firing three three dice primaries has a better expected damage return than three four dice ion cannons.
Just something to bear in mind. While three ion Gunboats are almost certainly going to rely on an ace to do actual damage, they are technically capable of doing some damage on their own, if you can fly them well.