I am not sure that the Excelsior is actually stronger than the Sovereign in game.
The tactical console layout is the same Armor is the same too.
The only distinction is the BO layout.
Which of cource under current implementation, influences the role of ships, which in my opinion should not but this is part of another discussion.
That being said, I have been flying cruisers since launch as a Tac officer. And when I compare the Assault Cruiser to the Excelsior, I actually have more survivability with the Assault Cruiser, because of its BO layout.
I still prefer the Excelsior but that is because I am Tac, and I think that with the excelsior I can at least put to work my career's skills (Tactical focus) more efficiently than in the assault Cruiser..yet, I do explode more often in it, as it lacks the capacity to withstand as much of a pounding as the Assault Cruiser.
So in that sense, even if it has one higher level TAC BO Power, it loses much on defense, which do make it consistent with what the OP actually wants. To have the feeling that the Sovereign is a Superior ship compared to the Excelsior.
I think it is, because it can stay alive longer than the excelsior, with similar weapon slots consoles etc.
What the game may need here, is a leap forward, we are 30 years beyond Nemesis, the Federation at War with the Klingons, if this were to be the case in the series, don't you think the the superb corps of Federation ingenuity and Diversity would not have come up with new designs to adapt to their new enemy?
Do you think that Federation would not have developed new ships cruisers,escorts and carriers even that can use same heavy armament as Klingons or match their maneuverability...it is really a no brainer.
There is lea way I think to come up with new stuff in this future of Canon Trek.
So I really think that the next batch of ships for the 52-61 Ranking should be a new Line of next generation Ships that are designed to respond to the Klingon Threat.
(Not unlike how the federation developed a bunch of ships to deal with the Borg threat, the defiant being one of the first of that line).
And in a way the Excelsior Refit can actually be a transitional step in the mean time until R&D and Construction of new designs finishes.