Phase teleport is huge game changer, and currently AI fails to adequately counter it.
1) AI raises omni shields a bit too late to block first shot after teleportation , which allows player-piloted Hyperion to pretty much ignore shields. Since freshly teleported Hyperion can raise shields quickly enough to block fire from target ships, reverse should also be possible.
2) It expects being able to raise 360 degree shields before Hyperion gets into firing range, which is usually false. Could be countered keeping shields up constantly if an enemy Hyperion is seen somewhere on the battlefield, though that's going to be big handicap against other enemy ships...
3) Ships which have neither 360 shields or omni need to cover each other and avoid staying alone.
Not sure about 2 and 3, but 1 seems feasible.