When I played the mission and got my Odyssey class, I noticed that it came with batteries (shield, engine, etc.) that recharged instead of being drained and dropped.

I now reach VA and unpack my package, still having that new ship smell, and they are gone. Did I miss something?

The ship you tested isn't quite the same ship you get to keep (note it even has a different ensign station). It has some filler equipment in its console slots and devices, which is mainly there to make up for the fact that you can't modify equipment on temporary ships. The ship you get just has standard issue equipment.

Note it also doesn't have the 20% diruptor armor or multi-system power console.

Sounds like I got it from a Used Spaceship Dealer and got fleeced...

Actually you got the final version of the ship.

The one you flew in the anniversary week was the Prototype.