Just a couple of thoughts.
Firstly, I've got to admit that for a supposedly superior race the bugs ships die fairly easily. On the other hand, the game has got to be playable, even by newbies, so don't complain too much until you're consistantly beating the game on 'you must be kidding' difficulty. Actually, I can just imagine the designers sitting down to plan out this game.
Designer 1 : "So, what's the plan?"
Designer 2 : "Well, I figure we have the player on patrol. He run's into this alien spaceship. It's from a race of super-warriors so it's twice as fast, has these guns that can kill you in a single hit, and its shields are inpenetrable."
Designer 1 : "Umm, won't that make it tough to beat?"
Designer 2 : "Yup, that way we only need to make 1 mission and a You Lose screen. We'll have this game shipped in a week!"
Anyway, back to reality, or at least our version of it. We seem to feel that the bugs aren't strong enough. What then are the bugs strengths? Hypothetically, superior technology and superior numbers.
First, lets look at numbers. It is theoretically possible the bugs have superior numbers. Their ships appear to be organic in nature, which could suggest that they are grown as much as built, allowing cheap, quick construction. This may mean sacrificing some effectiveness (a grown ship/weapon may not be as strong/damaging as a 'built' one) in exchange for rapid production. They certainly seem to have the numbers in most encounters. It does, however, result in some significant disadvantages, particularly with regard to the Midway. Firstly, the bug force you encounter is a scouting/beachhead force. They have no production facilities here, so their numbers are limited by how fast they can get ships through the jump gate, not how fast they can be produced. We have presumbeably seen only a fraction of their true numbers. Secondly, the Midway is a moving target, not a stationary one. She can pick and choose most of her movements/attacks. One would imagine that she would retreat, rather then face vastly superior numbers. For the bugs to bring their superior numbers to bear, they must first locate, then corner the Midway. The Kilrathi, who are presumeably trying to defend fixed positions, are quickly destroyed.
Now lets look at technology. The Nephilm will not necessarily have a vastly superior technology than ours, and there are many reasons for this. Firstly, as has been previously stated, war is a great drive for advances in technology, particularly those involved with killing other things. The humans and Kilrathi have been engaged in a brutal war for over 40 years. They haven't wasted their time, but have instead spent it perfecting their killing equipment. A single Thunderbolt could take down a squadron of Raptors without blinking an eye, and then have its arse handed to it by a Vampire. The Midway, while carrying fewer fighters than a Versuvius, is still chock full of the best fighters ever built. Even the 'lowly' Pirahnas and Tigersharks are still way ahead of their counterparts from only a few years previous.
In contrast to the Terran/Kilrathi war, the Nephilm have not (as far as I am aware) been involved in a major conflict against an equal opponent. Their technology, without a challenge or motivation, has been stagnating. Perhaps that is one reason why the bugs are here now. They have been here before (well, into Kilrathi space at least). Why not destroy us/them then? Because we weren't a challenge? or because they would have lost out on an oportunity to grow, and condemned themselves to further stagnation. They could have destroyed us without losing a single ship, but would have gained nothing in return. The bugs DO take out the cats, with their 'ancient' (read 10 years old) technology, with relativele ease.
Maybe it's just that I got better as the game progressed, but to me the bugs DO start with a technological advantage, one which decreases with time. When you first encounter them, the bugs are actually quite tough. Even though admittedly you are flying Piranas and Tigersharks at the time, even the Mantas and Morays are difficult to destroy. Your lasers and mass drivers hardly seem to scratch them. I know I usually had to resort to the Stormfire cannon and Charging Mass Drivers. Fortunately, the Midway's research division quickly picks up the slack. To me, your guns become more effective as the game goes on. The firepower of the Panther and Wasp are not enormously higher than the light fighters you fly previously (Panther : 2 Tachyon + 2 Ion = 482CM/S c.f. Tigershark : 2 Lasers + 2 Mass Drivers = 377CM/S), yet the Panther will chew through an enemy much faster then the Tigershark. I imagine your guns are 'tweaked' by the research division to make them more effective. Also, you gain access to the 'enhanced' missiles. Add in the fact that Midway steals the ship killer cannon and uses it to destroy a significant portion of the bug fleet.