Cryptic Studios has always been known for their customization since their previous games like Champions Online and of course Star Trek Online is no exception. Both your avatar and your starship is customizable from head to toe. An emphasis towards customizing avatars seems to be the most obvious similarities. Cryptic Studios puts emphasis in customization so that even though you have the same class ship, but you can still distinguish yourself from the other players. The concept is to retain the Star Trek look, while adding a touch of your own style. Just to name a few of the parts you can customize: the hull, nacelles, the saucer and the pylons. Of course colors and decals is part of the modifying frenzy.
Cosmetic decorations aside, you can upgrade weaponry, armory, warp engines, deflectors and all sorts of ability boosting upgrades that falls into the game tactics and gameplay. Different starships will vary from ship to ship by how they are customized, due to variable upgrade slots where you can add attribute boosting items. To make things harder, bridge officers that you assign to duty stations can give unique skills or a boost to systems. Progressing through the game will allow you to gain access to new ships and upgrades, so check regularly at STO Guide to see what is the next best new upgrade and customization techniques to optimize your fleet.