The real problem as I see it is that Cruisers are not high-priority targets in Escort-dominated PvP... They're too slow and their ability to protect other ships is very limited.
If Cruisers could more effectively protect other ships within their sphere of influence, then their threat level would go up, they would become more high-priority targets, and the ability to resist damage would be more critical.
THAT's what Cruisers should be designed and balanced around.
The only Engineering ability I can think of that can protect multiple ships is Extend Shields and it's not Cruiser-specific.
I think Cruisers need a specific, innate ability to extend some kind of protection to other ships. Something to clarify and improve their intended role in the game other than being damage sponges.
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