Howdy, all.
After a long time lurking, I finally decided to weigh in on this one, because of the rather surprising support for the WC3-era Kilrathi ships. I, as you might expect from the 'surprising' in the last sentence, much prefer the WC1/WC2 ships. I have three reasons, grounded in a basic (which is to say, not advanced) understanding of physics:
1) Asymmetrical engine placement. This is generally a bad idea, as it precludes flying in a straight line. For a particularly exaggerated example, consider a spacecraft with one engine, attached to it by a mile-long pole. The net result of firing said engine would simply be to propel the engine, not the spacecraft as a whole, and so it would circumscribe a lazy circle through space. The net result would be pretty similar for a Dralthi Mk. IV, for example, although the circle would be enormous, and if a pilot was making regular adjustments, it would probably be barely noticeable. Still, it would interfere with combat (though this could explain why Kilrathi only occasionally hit what they shoot at.)
This can be explained away by a variety of methods: unequal mass across the two 'halves' of a ship with one off-center engine, like the Dralthi, or balancing the thrust produced by two unevenly-sized engines, like on the Vaktoth. WC1 and WC2 take a somewhat simpler solution, though, in simply having symmetrical ships with symmetrical engines, which I tend to prefer, Occam's Razor being what it is.
2) Aerodynamics. Show an Air Force pilot a Paktahn, and suggest it could travel through atmosphere, and I would suggest he would laugh at you mercilessly. Or an Ekapshi, even, just in case some dialogue in the game precludes the use of anything other than those in atmosphere. (It's been too long since I've played it.) Fighters in WC3, for the most part, lack the lifting surfaces to sustain flight, though this can be overcome by their godawfully powerful engines that produce thousands of Gs-worth of thrust every second. That's fine, but the faster you're going in atmosphere, the less manueverable you're going to be in a dogfight. (The Confed fighters are also guilty of this, from WC3 on.) Of course, this wouldn't be an issue if these were solely space fighters, but WC3 disbused us of that notion.
The other problem is one of disruptive aerodynamics -- fighters like the Bloodfang and Strakha Mk. II (again, hypothesizing that these are capable of atmospheric flight to begin with) might be said to have claw-like wing things which could serve to provide lift, but the bizarre arrangement and unequal size would probably cause them to spin out of control immediately upon taking to the skies. WC1 and WC2 fighters, with even wings of some sort on most of the designs, seem far more viable in atmosphere to me.
3) Landing. Ok, this actually bugs me in all the WC games -- Kilrathi fighters seem to have no believable way to land. It started out well enough, with only the Salthi and Dralthi really problematic (and the Dralthi only because of those top-and-bottom mounted tail fins), but has gotten progressively worse, with various hooks and pointy bits getting in the way of any conceivable landing mechanism. WC3 is the worst in this regard, IMO, since fighters like the Strakha Mk. II or Paktahn would almost undoubtedly plant their noses in the ground as soon as they touched down. They certainly couldn't do it on a planet, and that's most troubling with the Ekapshi, which is supposed to be atmospheric and has that dual-tail thing. Not using artificial gravity on the flight decks of their carriers might solve the problem, but it creates a slew of new ones (such as the convenience of storing and working on spacecraft which can't be pushed against a surface.)
Anyway, that's my view on things. I'm not by any means suggesting that real-world physics should rule the Wing Commander universe, a universe where even the slow, unmanueverable bombers subject their pilots to better than 91,000 gravities at combat speeds.
I'm just saying such considerations play a role in my mode of thinking.
So, my money's on WC1 and 2. Give me a Dralthi any day. Though I'd rather have a Broadsword.