"Many have dedicated to "fixing" the problem. And as of yet I have not seen any mods that are any better than the stock game in that respect"
Mostly because when they (I

) start, they find out that A. things are a little better balanced than they thought and B. it's *hard* getting things balanced right.
Look at the APB. On a pure damage/kt scale, this thing is a monster- 2.3 damage/kt. However..it also costs almost 2 million research points to fully research, on medium tech cost. Something like the Meson BLaster, which does 'only' 1.75 damage/kt and is a bit shorter ranged, costs less than a quarter. In other words, you can have Meson VIs much, much sooner than someone can have APB XIIs. Mesons also have no damage dropoff.
The Wave Motion Gun. Costs less than the APB to research (true!) though you only get it at the very end of the research chain. Damage/kt rating of 2; damage/kt/turn rating of a less than stellar .67. However, you *can* run out of range with it while it's recharging, it does full damage along it's entire range, and it gets a 30% bonus to hit!
Quantum torpedo. Damage/kt: 2.5 1.25 per turn. Again, cheaper than the APB, if only because it has two less levels to research.
Missiles are a special case; they and fighters are weak because PD is so effective, not because they're weak in and of themselves. You can't saturate an enemies defenses when your weapons are twice as big AND fire three times slower.
Economy is very important BTW. Research center upgrades will get you that tech faster, miner upgrades (and computers) will put more ships in space. It's worthless to have the most high tech ship in the game if the enemy can field so many of his slightly lower tech ships he overwhelms and destroys you.
Phoenix-D