Kind of depends on what you're doing... if you're flying support with your engineer, I'd definitely say that the emitter array would be worth it (because it increases the power of your heals, but you may not be pulling mad aggro if you're flying support). That said, I fly a sci character and do a fair amount of running support (though much more focused on CC), but I prefer the higher capacity.
I steadily rock high-capacity shields, so a percentage boost to capacity is pretty significant to start with. I also have some skills/traits that let me (at least temporarily) heal up my shields almost the whole way... and having that 'whole way' be fairly big means that I can relax (and stay alive) when focusing on providing support to the rest of the team and locking down opponents. Also, the high capacity helps withstanding any kind of burst if you accidentally aggro a whole bunch of nasties and need to survive long enough to flee.
Now, I have a lot to learn, so I'm interested in what other folks think. Also, I recently dropped my shield-boosting consoles entirely in order to up my graviton and particle stuff, so maybe I'm not the best reference... that said, no one else chimed in yet, so...
To wit, I have a tac alt, but don't have a lot of experience flying Tactical... or an escort...
But, my understanding is that you want to get in, do a ton of damage, and get out... if that's the case, again, high capacity seems like a winner. Your heal increase will be fairly negligible in light of a whole bunch of (or a really powerful) enemies slamming you at once, but the higher capacity can help you squeeze through long enough to get out of range if you're really in trouble.
Again, depends on what you want to do... if you're mainly healing other folks, get the emitter array... otherwise, go for capacity. And, speaking of which, rock them covariant shields.
Unless someone comes through with better info, in which case, listen to them!