I'm not so sure that ACTA by itself is the way to go - a lot of the Victory At Sea stuff is probably worth copying through...
For example - in Babylon 5 it's rare that ships ever miss when firing.
Watch the series and unless shot down by interceptors or fired at (a) white stars or (b) fighters I'm not sure you ever see anyone miss at all.
As a result, it makes sense for the attack roll to be soley against the targets hull, whilst actually 'missing' is rare enough to be incorporated into the 'dodge' trait.
There's no starship engagement in the book, and the only engagement in the film is the Klendathu drop through fire from plasma bugs and king plasma bugs on the surface - which, whilst definitely 'not random fire' or whatever the quote was, misses as often as it hits.
Combined with starships packing big missiles as a primary armament (which, regardless of ACTA, are quite slow-moving weapons in a naval engagement; even in a modern 'wet' navy missiles have a flight time in an order of a few minutes at normal firing range) and I find myself leaning more towards the mechanics used in VAS for torpedos - i.e. stuff gets 'fired' during the shooting phase, then impacts later.
One difference might being having a chance to shoot the incoming stuff down if it's missiles and smaller plasma bug fire.
So the result is:
(1) place missiles in the shooting phase,
(2) once everything firing that turn is placed, you get to fire flak/intercept it with swarms of expendable bug 'fighters' (think the squids from the matrix protecting the drillers)/pray,
(3) anything left gets its chance to hit and punch through armour (and do critical damage if appropriate - although fed battleships and bug ships look different enough that seperate critical hits might make sense; an A/B/C/X/Y turret etc version for the humans, and a less rigid -attack dice for the bugs (since there's no single 'turret', you're just killing the plasma bugs on the hull).
Not everything should be interceptible; fire from king plasmas can - did - break a Valley Forge in half with one hit, and even a proximity detonation rather than a direct hit from an Ajax nuke warhead will be distinctly unhealthy for a ship or transport bug. (It's Starship troopers - there has to be the option for nukes somewhere)
As far as different ships are concerned, you have two starship classes between the film and series, and reference to more in the book (the comment is made about the fleet preferring regiment-carrying battleships to faster platoon-carrying corvettes as 'the amount of fleet crew isn't all that much less', suggesting that there's quite a size variation. Equally, the concept of a 'defender bug' as a sort of escort ship is quite possible, as is several grades of transport bug (the queen's transport bug was much tougher than normal, which is why they had to board it and blow it up from inside).
Boarding actions make sense. Drop shuttles can quite happily double for breaching pods, and/or one can imagine drop capsule equivalents used as boarding torpedos. An analogue for the bugs isn't unreasonable either (hullbreacher bug?) to deliver a swarm of warriors. For that matter, if having a load of vacuum-adapted hopper-esque things as fighters/interceptors, they could quite happily swarm onto a ships hull and eat their own way in....
There's nothing wrong with the ACTA boarding actions rules as is, to be honest, it's just a case of figuring out how to deliver the troops from one ship to another.
TAC fighters work fine for fighter units
Infested ships with hybrid bugs is another nice option.
Skinnies.....raiding ships, as noted, so smaller, faster things