While I'm a new player and I don't know first-hand how larger phase ships felt before this version - but harbingers and dooms that I've been experimenting with feel like overly expensive (cr, dp, supplies) shieldless bricks that cannot reposition themselves efficiently anymore, nor they are meant to trade blows w/o shields. I'd think that nimble positioning was essential for their general idea/role ?
The moment you turn phase you quickly slow down to a turtle speed, even with APC hullmod; Phase Coil Tuning doesn't seem to be changing/helping much (and its diminishing returns skills kick in momentarily - after 40 DP, so nominal bonuses are worth precisely 1 Doom; I'll double check if that skill works at all later) in case of AI control, it's actually amusing to watch it struggle as it tries to reposition a harbinger to hit the enemy ships from side/back and fail miserably - there's only so much you can do at speed slashed so severely.
The only option I found that somehow works with those two ships is SO, as it tends to offset the speed penalty (along with 0-flux boost always applicable in SO) long enough to let them reposition properly (and just barely). But SO cripples available ordnance, usage time, etc. ...
Anyway, "Phase cloak reduces top speed as hard flux goes up, down to 33% speed at 50% hard flux while phased" is a crazy brutal nerf. It's analogous to if some other ships felt too strong and something like "as long as your shields are up, top speed goes down to 33% speed at 50% hard flux while shielded" was introduced.