So the most likely cause of the Republic's doom are mines with cloaking or some other type of advanced sensor spoofing. Doesn't completely rule out sabotage or treachery (of sensors, for instance), but it's no longer as likely.
First things first, last I checked the E-A was still one of the most potent (if not THE most potent) ships around, and was likely to win a 1v1 match against just about anything. It'll compete quite favorably for a while yet, methinks.
This is both true and false.
True in that the elite USS
Courageous at C11 S9 H7 L9 P9 D8 is most likely the baddest mofo in the (Federation-)known galaxy.
False in that there exist ships that have superior base stat lines for the phases of battle that capital ships play in. The top contenders that we know of:
Starfleet Excelsior-A: C7 S6 H4 L6 P6 D6
Ked Paddah Aggadah: C6 S? H6 L6 P? D?
Rigel Megatortoise: C6 S4 H8 L9 P3 D3
Honiani Basilica of Lakhept: C8 S5 H? L? P? D5
Seyek Sign of Rethelia: C9 S6 H4 L6 P4 D5
Amarki Riala-A: C8 S5 H6 L9 P5 D6
The Aggadah is arguably on par with the Excelsior-A, and the Megatortoise, Sign of Rethelia and Riala-A are unquestionably superior at the battleship role. We don't know how the Basilica of Lakhept compares given its unknown stats, but at 4mt tonnage, it's very likely superior to the Excelsior-A, and possibly on par with our upcoming Ambassador.
edit: Megatortoise definitely superior as well (D is meaningless, S only slightly improves hit accuracy)
Then there's all the capital ships that we just don't know the stats of:
Konen Whisper
Padani Pathfinder
Horizonite Liberator
Romulan Khellian Heavy Warbird
Klingon Tar'chak
At least I'm confident that the Excelsior-A beats out the Cardassian Lorgot and Kaldar-bis
That all said, I completely agree with the rest of your post.