Not all of what I posted was canon.
Sovereign in mothballs:
This is stated in the Game Bridge Commander.
Not canon. May as well be fanfic in video game form.
The vessel was part of the same project as the Defiant and Prometheus. Sovereign was part of the "new class" or new fleet of ships aimed at replacing the aging Fleet.
Actually the Sovereign was borne out of the same design projects as the Defiant and Prometheus: with anti-Borg warfare in mind according to most of the ST:FC related official material I've found. Which you are correct in that the Sovereign was built to replace the aging Fleet... post-Wolf 359.
The low warp speed of Sovereign is observed by logical deduction in Nemesis...
Two experimental ships, Scimitar and Sovereign class Enterprise have an encounter.
Shinzon knows he can out run the Enterprise
Picard knows the Scimitar can out run the Enterprise.
-This means that Sovereign is not boasting a faster than normal top speed. aka 9.6 +
-In the Past Warbirds top speed was warp 9 with 9.6 damaging the engines. It's possible they have exceeded warp 9.6 with the 3 Singularity Cores to stabalize the ships SIF as well as maintaing power for speed and cloak. Essentially a core for each system. If this was the case then it would be much like a borg cube just funneling power enmass instead of using power efficient methods, like hull geometry for stable fields.
There's a flaw in your logic here, you're forgetting that the Scimitar was a Dreadnaught. Not "just" a battleship. And not "just" a Dreadnaught, but a Dreadnaught that would give a traditional Borg Cube or the Dominion Battleship a run for their money.
The fact that the Remans were able to build this monstrosity right under the Romulans noses defies all everything we had come to learn about Romulan Intelligence and the Military since the Romulan's re-introduction in TNG. Was the Tal Shi'ar on a coffee break for the years it took to build her? Were the Romulan Praetor and Senate blatantly ignoring the obvious?
It should be pretty obvious just from watching Nemesis that comparing the Enterprise-E and the Scimitar is basically comparing an Apple to a brick. I mean, the Scimitar is a single ship that can take out not only the Federation Flagship, but two Warbirds at the same time, all while travelling faster than one of the fastest classes in the Federation fleet.
It's a broken comparison.
Just because the Enterprise-E is apparently slower than a Dreadnaught that makes absolutely zero sense, doesn't mean that her max speed isn't in excess of warp 9.975 as it says it is on Memory-alpha.
-Sovereign's weapons shortcommings were obvious before the refit.
Why, because the Enterprise-E turned the tide at the battle of 001 and dealt the killing blow to not only the cube, but also the sphere? Because the E-E destroyed one Son'a battleship and crippled another in quick succession before disabling a Son'a crusier?