I, personally, prefer to fly an Apogee - though I haven't yet managed to get one in the current version of the game. Its big advantages are decent mobility (with full skills it can outrun some of the slower frigates), exceptionally strong shields, and superior range; as long as you can keep your drones alive, you can outrange almost anything. And the only things that can threaten your drones while your shields are up (and they're holding station - never use roaming mode) are ships with EMP generators (and a few AoE weapons - bombers making a run across your shields can kill your drones as well.)
The Apogee's disadvantages are its relatively few weapon mounts, and the odd placement and inconvenient firing arcs. Even against other cruisers, it's difficult (and frequently not worthwhile) to get more than one of your medium turrets on target at once; combined with the turrets being at the back of your ship, it's often best to approach an enemy sideways rather than head-on.
Due to these drawbacks, a solo Apogee is a bit vulnerable to fighters, especially broadswords; if you're up against a fighter heavy fleet, you often have to spend a significant amount of time maneuvering until you can either take out the carrier(s), or until the fighters simply run out of spare hulls.
At low skill levels, I find myself using heavy blasters and burst PD, all on autofire, and with plenty of use of the hold fire button to let soft flux go down when the heavy blasters drive flux levels too high. The rest of your ordnance points should go into unstable injector, max vents, dedicated targeting core, and some capacitors.
Given the buffs to missiles, it may also be worthwhile to add a swarmer launcher to the above loadout, probably at the cost of some capacitors; anything you can do to better protect yourself from fighters is probably a good idea.
That stays pretty much constant while I gain levels in combat; the key skills are speed boost, dissipation / shield efficiency, and of course the damage boost one that ends in reduced ordnance point costs. (Oh, and you want the level 5 perk for +75% maneuverability, but there's no need to push that skill any farther - if you play right, you won't take damage to armor or engines in the first place.)
Once you hit combat 10 and have some extra OP to play with, I tend to add one autopulse laser and call my armament done; after that it's time to bring up tech skills. Key things to get are stabilized shields, more ordnance points, and the extra range boost from gunnery implants. The autopulse is a perfect choice to pair with the heavy blasters; it's highly flux-efficient, and the way its ammo regen works means you can unload a burst and then turn to bring a heavy blaster to bear while the autopulse regenerates charges. (General rule of thumb, though: don't bother firing the autopulse at armor on anything cruiser or larger; use it to raise your enemy's flux levels, but use the heavy blasters to break armor.)
There is one other Apogee build that I have a lot of fun with, but it basically requires being good at mouse steering (and having at least combat 10 and tech 5): Mount a plasma cannon. Assuming you can hit frigates with even 50% reliability, that one plasma cannon will deal with anything that's not a fighter - so you can spend the entire rest of your armament on dedicated anti-fighter weapons; I typically use turreted phase beams and tactical lasers, backed by that AoE medium bomb launcher that I can never remember the name of (used to be phase charge launcher, but then the "phase" part got dropped); slap that in your large missile slot, and use it exclusively to deal with large swarms of fighters.