@ TaLaR: What I meant is something like enemy expedition attacks one of your patrols in your system (with colonies), and you want to join the fight-in-progress. It is like expanded battles except your ally is one of your patrols, not Hegemony's, Tri-Tachyon, Independent, or other faction. If I want to use my patrol as disposable heroes (by letting them do as much dirty work as possible on their own) I do not want phase ships that flit about and do nothing before their CR completely burns out much faster than other ships. And I would not want sub-par hulls that are clearly at a disadvantage in a fight if the player is involved. I want simple bruisers that efficiently smash whatever is in their way.
Normally, I would not care what my patrols use since they auto-resolve fights, much like player can do in pursuit. Player can use utility ships in pursuit and they easily destroy ships they would have trouble doing without dying in a manual fight. However, there is the current fringe case where player joins a fight-in-progress. In 0.9a, player can completely ignore manual fights, and should due to rep penalties. Maybe it will be more common in 0.9.1 due to various changes.
EDIT: Occasionally, I have looted what is left of my own patrols (who died defending my colonies from expeditions) for cheap ships and free weapons. Controlling that loot via priority is handy.
As for phase fleets, I think HELMUT said having a pure phase fleet was not fun. I had not tried it, but I can see why. I do not bring phase ships unless it is Doom or something I will pilot often. It is painful watching AI pilot any phase ship that is not Doom.