You don't have to "choose" between any of the three governments.
Technically, you can't even join them.
So feel free to rank up to Baron with the Empire to purchase an Imperial Clipper and make Ensign with the Federation for the Dropship if you like.
You can hold Ranks with Empire and Federation and be Allied to all three governments if you wish.
Every Player basically remains an independent Commander, regardless of Ranks or Reputation earned with any Faction.
Apart from the two above-mentioned ships, all other Ships are currently freely available to everyone.