I assume it's something to do with the new warp cores. The only one I've been able to find is one that boosts aux power, but i think there are ones that increase shield integrity and hull resistance too.
Look on the exchange for the different types of Warp cores that's what i'd recommend for you.
The other thing i can recommend is switch out your offensive engineering abilities with more supportive ones, Such as engineering team.
"We won't go back, you don't know what its like in our Universe, the original timeline had gone, JJ Abrahms is everywhere"
It does seem that Cruisers are, overall, a bit more vulnerable now. This could be that innate stats have been lowered, or that the behaviour/power of enemy NPCs has increased. This may be a result of the equalisation of EPtX powers (a general improvement across the board), or as suggested above, it could be the Warp Cores.
Note that the Engineer-specific space trait "Grace Under Fire" now means that you can feel comfortable using Miracle Worker without worrying about the enormous cooldown.
Ive found with my odyssey ops cruiser that reverse shield pol is a lifesaver, one hit from a borg weapon in eleite borg task force can completely regain my shields (although it doesn't protect from torpedoes but i have beam fire at will for that) and and attack pattern omega and hull plating in one of my science can keep you from being caught in a tractor beam.
Hmmm, my ops ody and ACR are doing well since romulan go live if anything my cruisers are better with the emergency to x power changes and trait system if anything I rarely use miracle worker even in elite STF's.
I haven't noticed this so much on my shields as I have on my hull. I know that the leadership trait was "corrected", but even with 5 human boffs with the trait I've noticed that my hull doesn't seem to repair in combat, only out of combat. After LoR came out a few people in Zone chat independently commented on this throughout that night.
I mean even before I got any human boffs I didn't die with full shields on each face from bleed-through (especially since I have the Jem'hader resilient shield). I pretty sure that before I had the leadership trait at all that my native hull repair was much better in-combat than it is now with x5 Boffs. I was going to start a thread on it at some point and see if anyone else noticed this, or ran some numbers.
I think resistance stats and hull HP have been boosted again for the borg. I guess it was made to balance out the additional powers through the trait system. Many escorts can still overcome it with raw firepower but cruiser have a harder time then before.
I've seen Escorts pop from a Cure Elite Cube's HY torpedo despite full shields since LOR.
Taken 49k crits from them as well through shields. So it seems they've got the 'invisi-torp' levels of damage but at least they're visible now. (As do the Raptors with their HY torps.)
That's really the only change I've noticed although NPC's in general seem to be doing a bit more damage. Makes things a bit more interesting now. Resistances definitely weren't buffed, I deal the same amount of damage.
Leadership not buffing in-combat regen might be a thing though. Out of Combat regen is fine for sure.
As a Cruiser Captain, I only have a little bit more difficulty than before. (Mainly because Tac Team keeps going on my freshly-launched Romulan Plasma Torpedos rather than myself.)