Personally as a section 31 officer I would love to have a Black Hull Option , I know this is not really a ship design but hey it would be cool........ I notice that the new console that comes with the "Rhode Island" gives you a black hull while the decoy ship is about, so this is already in game and should be easy to do... at least for science ships.
As for ship classes..
Wells Class is a must as is the Duantless, fingers crossed for one or the other.
1. The Raven released as a kind of large shuttle-type craft (the one from ST:VOY; The Hansen's ship).
2. The ability to collect various mission-related trophies to decorate your ready room or quarters with (not like the current kill or FA trophies but objects of some significance like McCoy's Medical Tricorder (from when you meet him in "Everything Old is New") or an (albeit small) chunk of the Doomsday Device to put in one of those "suspension / floatation frames" (as seen in ST:VOY - Year of Hell; what the antagonist has that last remnant of his homeworld in). T'would be cool. After all, canon captains set the precedent with their little nick-nacks - Picard's pan-flute thing, Sisko's baseball, and Janeway's beloved coffee cup!
3. The ability to meet and interact with canon characters, maybe even bring some into the main storylines, like Janeway (a MUST!), Chakotay or Will Riker. Pretty much anyone except for Luxwana Troi or "the boy"!!! Meeting McCoy and Scotty in the Devidian series was really cool. More like this would be fun. I'm pretty sure Admiral Janeway would work well as the head of (a newly revived) Starfleet Borg Taskforce.
4. Linked into point three, it would be good to have some unique Borg counterparts to give that antagonist faction a bit more character. I know we're supposed to be getting the Queen with the release of "Into the Hive" but having other counterparts underneath her as kind of senior henchies would be fun. Think of how ST: Armada pulled off the ressurection of Locutus; or how the CCG game did the special Borg counterparts (Gowron, Boriel, Tomalawk).
EDIT: Just noticed this was a ship-only wishlist. My bad. Oh well, the above still stands.
Not only "Yes", but a "HAIL, YEAH!!". I've always loved the New Orleans-class. I always felt it bridged the TOS and the TNG better than the Enterprise-D did.
I've also always had a soft spot for the Larson-class destroyer from the old FASA StarFleet Battles game. This is the USS Richthoffen , one of the first Larson-class ships I ever found on the net, over 10 years ago now.
I think three great Federation ships would be the USS Relativity (the future ship from the Voyager series), the USS Pegasus (from The Next Generation series) and the Yellowstone Shuttle Class (From Voyager).
A ship for both KDF and the federation could be an Alice shuttle (Voyager series) that had neuro-mematic controls, it allowed Tom Paris to control the shuttle with just his mind. In the game it could have great maneuverability, speed and an ability where most shots taken at it are missed.