sure i would like to have more weapon slots on my retrofit intrepid too but then i'd be flying a speed-crusier that'd way too overpowered! 3 fore, 3 aft is just balanced ... besides you have enough abilities that should give you the edge over any enemy on your level you encounter
you can't be a wizard, tank and hitter, all in one ... and if one role doesn't suit you, pick another or pick at least a cruiser/escort ^_^
i appologize ahead of time if what im about to say has already been said in other posts in this thread...
i have ZERO problems in a cruiser keeping the enemy on my side for the full broadside dps. I do this with RCS consoles. granted i dont turn as fast as a science ship similarly equipped or even an escort, but i still have ZERO issues broadsiding targets. and since a science ship has a better turn rate than my cruiser, the lack of an engineering slot (or 2 depending on the endgame ship hull you use) should not matter compared to a cruiser.
all the above said, a science ship, since it is science skill oriented with boffs and consoles alike, means your dps is more related to science skills. there is one good actual dps science skill, gravity well II (or III if you have it) as for the rest of the science skills, i look at them this way: if they debuff the enemy's dps output capability, that equals dps on my part, since i am preventing them from killing me faster than i can kill them. tractor beam, repulsor beams, that one space knockback one that looks sort of like a small concussion wave emitted 360 degrees from your ship, etc. all these can prevent the enemy from doing dps on you, which increases your dps by not having to blow science skills on heals.
it is my feeling that a well-played science oriented vessel can, over time, very nearly out-dps even escorts, by preventing escorts from out-dpsing them. prevent the escort from moving/turning, and you can bring your broadside to bear. if you cant prevent him from moving (those skills are now on a cooldown), then the next best thing to prevent him from DPSing you, is the poor-man's cloak, jam sensors. if they cant target you, they cant dps you. this means you can be dpsing on them and they cannot return fire. if you can time all of these properly, you can bring down the target's shields (especially the pesky escorts) and spank em at least once with a tri-cobalt or a high-yield torp barage, or even a plasma torp. heck, if you can bring a shield facing down and drop a transphasic cluster torpedo on top of it, its likely to do alot of damage as well.
there are many tactics to playing this game, you just have to play to the strengths of your loadout.