Under player control I feel the opposite, Grendel has it's moments and excellent burst weapons but suffers from low speed (you get bullied by High Intensity Lasers, so cover is needed), but Harbinger with 3x Phase Lance (under player control and appropriate skills!) and a DPS-focused build can work around just about anything simply because of much higher speed and phase stats as well as good range from Advanced Optics + range stacking. You can dodge just about anything at ~1000SU and Phase lances let you abuse shooting corners easily.
But I do agree completely that under AI control it's shockingly bad, especially without officers. AI wastes the ability on inappropriate moments (it should count in bombers/torpedoes/potential DPS for the next second coming in on the target), lacks in survivability with questionable decision making (like cloaking under kinetic fire and staying cloaked, no rapid cloaking->uncloaking in some circumstances with Phase Anchor, tanking "low damage" autopulses without cloak) and doesn't have the game-breaking speed Afflictor has to control every fight. Armor helps a lot but is less important in my opinion.
Ideally, Harbinger behaviour should be sort of "fire and advance", cloaking at 0 flux to get within range, let out a burst, cloak again, using it's ability in between then repeat. Venting only while withdrawing from target or if enemies can't punish with beams and missiles. It should kite when there are faster enemies nearby but not spend too much time phased.
I'd like the ability get buffed to 2 charges (or even 1 charge so it stacks with SysExp) so you don't 'waste' charges by not using it or the cooldown decreased to 18/15 seconds, or do the inverse - increase cooldown but also increase how long target ship is overloaded. Range should be extended to 750SU instead of base 600 at minimum, with Escort Package or a range-focused Phase Lance build my weapons outrange the ability. It could also open up defensive use of the ability - I shock the enemy to cancel their high burst weapons so I can recloak or vent safely.
Even then, there are simply no good weapons to alpha with - downsizing medium slots to AMBs is technically the highest burst, but Afflictor (or even Shade/AfflictorP) does that much better, so why bother? Phase Lances don't quite fit - too long active phase, not concentrated enough burst (cooldown to active proportion). Heavy blaster doesn't do enough with single shot and can't guarantee landing two (you may be able to corner-shot, exploiting the fact that AI raises shield in exact direction to target). Etc.
If we ignore Harbinger's system, phase anchor flux dumping playstyle would require same high burst energy weapon that doesn't quite exist to truly shine.
On that account, using the Scalaron Blaster (Blackrock) and Animus Blaster (ORA) from modded on Harbingers I've found great success versus larger ships when it comes to disabling systems and cracking armor, they stack great with damage buffs and Phase Anchor! but I always went back to Phase Lances because it also doubles as a decent PD weapon to manually shoot down missiles and fighters with and the safety granted by range buffs. A good burst medium energy weapon would do a lot to improve the effectiveness of AI Harbingers, I agree.