Actually...
Tomahawk: The probability of a precision hit is very dependent upon the opponent's countermeasures. Against an equal adversary, the Tomahawk would prove much less effective than it is against third-world opponents. Our own Tomcat, with it's twenty year old Phoenix missles, could stop a half-dozen Tomahawks in their tracks(and has, in field tests of the Phoenix). The Navy has a wide variety of anti-air weapons designed for the sole purpose of destroying incoming missles. Even then, the average ALCM has a CEP of around a hundred meters...that is, on average, about half of all of the missles fired that make it to the target will land within a hundred meter radius of the target. (More modern GPS guided munitionscould be more accurate...that figure is for a 90's vintage ALCM. Of course, you can try to jam the satellite transmissions...)
Laser-guided bomb: Smart bombs are dependent upon a targeting system that is vuulnerable to atmospheric disturbances, and their textbook accuracy can suffer a lot when the pilot painting the target is busy dodging SAM's and groundfire. They are also much more expensive than conventional munitions, so are not used as much. (90% of the bombs dropped in the Gulf War were just dumb iron bombs) And any bomb is only as good as the pilot dropping it. 80% accuracy seems pretty optimistic to me, at least against a well-armed opponent.
Mines: Mines are actually a suprisingly effective weapon, and get smarter all the time. They lack a lobby group, though, so they are not popular with the military and develop much more slowly than other weapons. They have never been very good at distinguishing friend from foe(one reason they are so unpopular), but are improving. By the 24th Century...who knows? But the effectiveness of countermeasure will probably keep them too dumb to play well with others.
Rifle: For every good sniper, there are several dozen G.I.'s who just hold the gun up over their heads and spray away.
While it is a truism on the modern battlefield that what you can see you can hit, and what you can hit you can kill, it is a matter of historical record that evenly matched opponents with a similar state of technological development will find themselves locked in a tug of war between measure and countermeasure that will insure that no weapon system will be 100% effective.
Of course, it's a game, after all. It seems rather laughable that two spaceships travelling at super-light speeds (an impossibility, anyway) would be engaging in artillery duals within eyeshot of eachother. And how do you hit a ship travelling FTL with a beam weapon, anyway?
All that being said, I think you have some valid points: Seeking weapons make a lot of sense, and the defensive weapons to counter them would create some interesting ship-building dilemmas. I miss missles, and transporter-bombs, and pont-defense systems from SFCII. They provided some interesting gameplay options. (You could argue that photons and the like ARE seeking weapons, though...they just don't always work) Given the frame-rate hit of shuttles, though, there may be a good technical reason for excluding them.
I think mines should still have the rings, though...of course, you could say that only DETECTED mines would generate rings, and only for the person who detected them. That would make things interesting.
Klingons DO need something more effective in their arsenal. (A more impressive looking Dreadnaught would be nice, too, but that's not Taldren's fault)
Oh, well, great post. Anybody else with some thoughts?