For player piloting I'm finding the Harbinger to be the best. Better than Doom even, but I suspect that might be a skill issue on my part as people report doing things with it that I can't in a Harbinger. I can't just rock up and 2 shot a Radiant in the H like the 8x amb doom can, but at the same time I'm so much faster in the H that I can get a lot more smaller kills, faster, with no ammo constraints. I'm still working on it. There are lots of other good player flagships too.
For the AI: Phase ships (afflictors in particular) are excellent in AI hands when given frequent orders and supported by the phase skill (phase ships on an assault (right click assign on a capture or give an actual assault for other ships to go too) or eliminate command have entirely different movement logic than normal, it seems). The AI works with the triple phase lance Harbinger, but I have not tested it extensively enough to know if it is good enough to be worth the extra DP as I've been flying it myself.
For lower micro, stack up on the missiles in groups linked to guns: Conquest, Gryphon (Legion too, though not quite as good!). See a bunch of Vanshillar's posts for builds and lots of data! These are probably much better than phase, but I don't have numbers to say how much. The Conquests back up missile spam with long ranged guns to pop smaller targets that might evade squall/locust/harpoon spam.
Would phase on top of conquests work even better? I'm not sure as my phase testing was part of a high tech themed playthrough. The 50% damage boost from afflictors is certainly attractive as a support to missile spam and they are very efficient in killing stragglers. Plus having a phase component makes the AI ball up, which is not a winning strategy for fighting Conquests!
Onslaughts, Executor, Legions, and Eradicators are all good for their costs. The Onslaught especially in player hands, the Legion/Executor especially in AI. Sunders make great fire support escorts if not going missile spam (which is better) as with escort package they have incredible range. Medusa make great distraction tanks with moderate firepower - more like hypermobile and decently armed Monitors that don't work via being outside AI expectations, rather than being firepower based.