I think if I had purchased an EFI motor originally, I would not have felt the need to repower. Yes, a 90 is a lot of motor on a 16, but it's nice to have the additional power when crossing the bar.
I'm surprised you wouldn't want to go with a SR 21. That is one of the nicest riding small sea boats I've fished. We took a friends 21 tuna fishing, and ended up 63 miles offshore. I've not fished a skip tower, but the headroom looks nice! When I had my SR 17, my first power boat, I found that anytime I took a splash on the fore deck, it would shoot up between the windshield and vinyl top. I don't know if that would happen with a skip tower. I guess it doesn't mater, because anytime it's that rough... I'm staying home now.