Taken from the Databanks under the Republic Assault Cruiser Profile:
Cruiser (Venator-class Star Destroyer)
Also taken from the description:
The front half of the ship's dorsal surface contained a massive flight deck capable of scrambling the latest in Republic starfighters. The huge hangar doors opened to allow ships to land or takeoff from the deck; the vessel also had a smaller docking bay entrance on its ventral surface.
I suppose that would explain why the ships are pretty lightly armed compared to contemporary Federation and Separatist ships also listed there.
Okay, but that still doesn't tell us what the ships in the end of the movie are, at the Death Star scene.
There's an article in the latest issue of Star Wars Insider called The Starships of Ep III. It's a Venator-Class Star Destroyer. From the snippet on this ship:
"There's no denying it now - we have STar Destoyers in the prequels. The triangular transport ships seen in the closing moments of Attack of the Clones were cool but were merely embryonic versions of Episode III's new Venator-Class Star Destroyers. They are the most powerful capital Ships in the Republic navy."
And then it goes on to describe it. Can carry more than 400 fighters, 40 gunships, 2 dozen military walkers. Crewed by over 74000. The Venator is 1100 meters as opposed to the Victory Star Destroyers 900 m, which the article says also existed during the clone wars but are not seen in Ep III.
The VicStar is a space superiority vessel... since all of AotC combat was on land, their absence is not noteworthy... RotS is another question. However, given they are probably a new and powerful ship, they would probably have been deployed and actively fighting the enemy, since the Republic probably never anticipated an attack on Coruscant.
Wasn't there some Venator Star Destroyers in the last Clone Wars episode that might responded to the attack at Coruscant? Should we have the ships from Ep3 under Imperial rule here? Those new separatist ships had only a few hundreds of crew population.
The ships that you're refering to are probably more likely to be the predecessors of the Victory-class Star Destroyer rather than the Imperator given the fact that they can enter gravity freely.
Victory Star Destroyers and Venator Star Destroyers both existed during the Clone Wars, but what we see at the end of Ep III is the Venator. The ones in Ep II aren't really Star Destroyers, just troop transports shaped like them.