Ship Types:

I currently have in my head the concept of 3 Types of Ship. Command, Exploration/Science and Combat.

Command:
'These are the Voyages of the Starship Enterprise'
These will be the Classes that have born the name Enterprise. These will have a 'Factory' Style lab (With no Construction Access) So they can gather resources from other ships and planetary sites. They will also be better than science vessels when it comes to combat, especially survivability. So you get a mix of 'both worlds' with the Command classes.

Planned Classes:
Constitution
Constitution - Refit
Excelsior
Ambassador
Galaxy
Sovereign

Exp/Science:
These ships will have 'solar panel' labs and will produce research/resources simply by their continued existence. They will probably also have 'Factory' Style Labs to be able to conduct planetary research missions and the like. (Possibly only for the larger Classes.)

Planned Classes:
Oberth
Miranda
Constellation
Nebula
Intrepid
Nova (Possibly)

Combat:
These will shoot things, you get that right? Chances are, at least for the Federation, these will all be late game ships, because they all come late in the Timeline of Star Trek.

Planned Classes:
Saber
Steamrunner
Defiant
Norway
Akira
Prometheus
(Or possibly a Lokota Class: Excelsior- Refit) [That is a less interesting shape though]