^From the in-game codex: -
* CAPITAL SHIPS are Sovereign-class Reapers two kilometers in length. They typically target the dreadnoughts, defense installations, and industrial cities of organic civilizations. Experts believe the Reapers harvest a single species of organics during each cycle of extinction to create these massive ships. Some capital ships are capable of launching small drones equivalent to fighters.
The thing you kill at the end of ME2 would just have been the central core of the Reaper, like the one you find Legion next to in ME2--which was also shaped like a lifeform. The 2km long hull is a shell that gets built up around it.
I think EDI even mentions after the Tuchanka mission that the destroyers appear to be of a uniform design, the Sovereign-class Reapers are all uniquely constructed (though, of course, still very similar.) Actually, that's something else that bothered me. At the end of ME2 you see the full Reaper fleet with some very different looking designs, but in ME3, all we see is the ones that look exactly like Sovereign and the destroyers (plus a cameo from Harbinger.) I realise there's a limit to how many assets they can use in-game, but I'm sure they still could have been used in the pre-rendered scenes.
As for your last point: -
...while going through that pastebin, I noticed what looks like data for new weapon mods. The Assault Rifle Omni-blade, SMG High-Velocity Barrel and Assault Rifle Thermal Scope caught my eye. That's assuming this *is* new stuff of course. I suppose it could just be cut content.
These lines of dialogue also caught my eye: -
"What is it with you and rescuing scientists from dig sites that have been overrun by hostile forces?"
"If you decide to help her take down the Shadow Broker, I'm going to be jealous. And somewhat concerned."
"Not that I'm complaining, mind you."
"I'm glad you made it back... and I'd appreciate it if you avoided talking to Leviathan any further."
"I don't want any tentacled creature inside your mind... except me."
^I'm assuming that's all Liara.
I like how they've given her a sense of humour in ME3.
Oh, and : -
"That mining facility... everyone there under Leviathan's control. It reminded me of Feros."
Perhaps that old theory of a link between the Thorian and the origin of the Reapers still has some life left in it after all!