the Gila Monster [...] has been quite sad.
I felt the same way. I've been running a lot of simulations with the Gila Monster against other battleships, and I have tweaked its stats considerably. It now has the potential for quite a bit more damage output than it did before, but even with all the improvements, it still does terrible (on its own) in situations it was not designed for.
For example if you run a sim now with the standard Gila vs. a standard Onslaught one-on-one, the Onslaught does the same thing I would do, if I were in its place: activate the burn drive, close the distance as quickly as possible, and flip on the auto-annihilator payload unleashing hell. If you fire into the hail of rockets directly, the doom cannon will fizzle out on one of the warheads while the Mark IX's and TPC's whale on you, and you will lose. The secret is to shoot askance, at one of the flanks as far off to the side as you can manage. Because if you manage to get a few shots through, it'll overload his systems. If you still have enough flux remaining (which isn't a sure thing) you can finish him off. If you elect not to use the Doom Cannon right off the bat, you can rely on the PD weapons to destroy the annihiliators until they're exhausted, and then go in for the kill, but this too can be a problem. So in conclusion, Gila vs. Onslaught head-on is possible to win, but the Onslaught is still properly scary when it wants to be. That's exactly what I want.
Versus a Paragon, the Gila is still lacking. This also fits with my desired lore; everything about the Nomads is a sort of branch of low-tech designs. Things are built simply and built to last. The Paragon is from a completely different mindset, and really I feel it ought not to be taken out so thoughtlessly. If you want to take down a Paragon, you'll need to put the Gila into a support role and bring it in to finish off the Paragon when its flux is already high. For this purpose, I've added an additional flight deck to the Gila, so you can field more fighters in this way. It's also important to use the High Energy Focus ability to squeeze every last bit of damage out of the main cannon.
Against the lesser battleships and cruisers, one on one, there is no contest: Gila annihilates them. Versus multiple faster cruisers, it gets dangerous very quickly. Even against multiple slow cruisers, like Dominators, it can be a tough fight. It is still, however, fairly expensive to have in a fleet, and expensive to field in combat. It has its role in a fight, but you'll generally want it with an escort. It's also important to use its directional shield as much as possible.
In conclusion it's getting there now, but I feel like this fleet still has some gaps. For instance I still have no cruiser-class ships (oddly enough) and no strike craft. I'm planning on tackling these roles soon, after the next release.