I have the same dilemma. For me one of the most enjoyable things to do in the game is to custom build my own ship with the best possible modules and then doing the engineering upgrades. As it stands right now, my Fed Corvette is the "end all be all" for combat, the Type 10 for mining and cargo hauling, the Asp Explorer for exploration and the Cutter for when I want to simply travel in style and pretend I'm some sophisticated member of aristocracy.

All of my other ships like the Anaconda, Python and Krait Phantom are extra ships that are just nice to have just in case I get the itch to fly them.