Having the hyperion as a flagship is a great idea. Say for example, when your conquest is struggling against an onslaught
you can easily teleport to the back, switch to AMBs and shout "prepare your ***holes"
if you have enough missile tech, you can even get four reapers on this badass, which can kill any ship (except paragon) insanely easy
Most recently, however, I've switched to Afflictor and I believe it is a better choice.
If you have enough level (and a lot of OP), you can fit it with 2 reapers (4 if missile tech), 3 AMBs, augmented engines, and even auxiliary thrusters.
with the rest spent on max flux capacity and dissipation.
This way, I can use phase to fly past an entire armada (like its not even there), snipe a few buffalos, hounds and devastate the onslaughts before retreating to safety at a speed of 250 (300 w/ boost) and venting flux.
I find the cloak useful specifically in cases when you don't want to be caught in the explosion of larger ships.
The cloak activates faster than the teleporter.
comparing to the hyperion, it also has considerably more armor, hull and flux level.
The hyperion is superb however for capturing nav buoys and pursuing frigates, so I still need a few of them in my fleet, but I'll just leave them to the AI.