I haven't tried the SFB-Starmada crossover rules, but you're misremembering plasmas in SFB badly.  The Plasma-S in seeking mode could knock down just about any shield a cruiser carries out to range 10, and was serious damage out to 15-ish.  If you were running away from it at speed it was less of a threat, but closing just extends the high-damage threat zone.  The two plasma-S torps on a K5R ought to take a frigate and (barring a weasel) crush it like an eggshell if you're modelling SFB even semi-accurately, and that's without the little plasma-F torps the refits added or the phaser array firing.

No frigate should be able to hold up to a cruiser.  If the point values are making them similar in value, there's something wrong with the translation between systems.

For one-off games, adjusting the VP cost of expendable stuff by a significant factor might help, but you'd have to include an increase of some kind for ships with One-Shot and/or Ammo weapons as well.  Hard to say what an appropriate increase might be, it's likely to be very situational.  Slow weapon users might need a bump as well, but I doubt it - I've never seen the level of problem with them I have with extreme striker/fighter/one-shot fleets.

Perhaps stop treating the Ancient ubergun as a single wepon, then?  Buy as many of them as you want/need/can fit, give the a home penalty trait that prevents them from firing at multiple targets (or did that one finally show up in a supplement somewhere? - I can remember arguing about including it as early as Compendium), and call it a single weapon that degrades with damage rather than an all-or-nothing megacannon.  Bit like the mid-period spinal mounts, without all the weird quirks.

Regen is also a decent way to model any kind of power absorbtion defense - black globes, Andromedan PA panels, and maybe these energy diffuser things - where a ship can soak up damage for a while but falls apart quick (or explodes) when the capacitor is finally overloaded.  Just think of "hull" as being "capacitor space remaining" instead and your regenration becomes the amount of energy bled out of the batteries that round.  The ship's actual hull strength is kind of meaningless, since most ships with this kind of defense pop like soap bubbles when you finally overfill them - usually with some "leak" damage bleeding through beforehand, which covers the gradual degradation of weapons/shields/movement as well.

How huge is huge?  The launch rate restrictions limit how many any given ship can put in the air per turn, even with launch tubes.  Yours are kind of high-end and operate in big flights to minimize that, but how many were there, and did the enemy fleet have fighters/strikers/seekers of its own built for defense against that sort of thing?

That's what we should have done with Space Fleet Omega years ago.  Before the wiki got trashed it was growing into a perfectly good setting for a game, and still a great in-joke.

No, only double.

But you have to admit it would be funny - about on par with the old GURPS: Rifts sourcebook joke in Murphy's Rules.  Or perhaps Candyland of Cthulhu. 

Khurasan also makes the Green Slime:

http://paintedterrain.com/PaintingPortfolio.aspx

Stat those up while you're at it. 

Take a look at Battleshift here:

http://web.archive.org/web/20071113031207/http://www.thanesgames.com/battleshift/bsmain.htm

One of the few games I've seen that incorporated tactical hyperjumps right from word one, and fairly good at it too.  Easy to crib ideas for Starmada, especially since you're plotting movement anyway.  Thane's site is gone but the archives still work, albeit slowly.

If you're really trying to model FS:A as accurately as possible, the datagroup sizes should correspond to the maximum squadron sizes in the original game.  Having larger squadrons is a major edge for races like the Sorylians and (to a lesser degree) the Aquans, and that should be reflected in a port.

OTOH, the more I've played FS:A the more I question why anyone would want to.  The universe isn't that compelling, the rules are full of typos, the design system is easily broken, and the gameplay is about 50% slower than it needs to be because of rotten design.  Better to chuck the lame vestiges of the parent game and just stat the (relatively) cool ship minis to suit your own play style in Starmada.  Even then I don't know how you'd ever play with them on a hex map, but Starmada does work gridless as well.