Right now the ships are balanced such that, in theory, each one you unlock with rank is slightly better than the previous one, with things mixed up a bit to keep things interesting.
However, since most players will unlock all the ships rather soon, it might be a bit better to modify this paradyme so that the ships of a given "Tier" are balanced with each other.
My thought being that there are basically 3 ship categories in each tier.
There is the Shooter (all guns, big armor and hull) Carrier (2 bays, less guns,armor,shield), and the inbetweener Cruiser (1 bay, 1 less gun).
Hence most start with one of these 3:
Armada 2000 / 600 5 gun, 0 bay, 8 PD.
Liberator 1000 / 500 4 gun, 1 bay, 7 PD.
Valhalla 900 / 500 3 gun, 2 bay, 6 PD.
In theory these should be balanced with each other. It seems that depending on how much one values a Fighter Bay over a Gun Turret, that the Liberator kinda gets the shaft.
I would expect its armor to be closer to 1500 maybe with a 550 shield. Oddly, even though it is higher ranked than the Valhalla, it seems weaker overall.
Then, as far as purchasable sidekick ships, I would expect to see the next "Tier" down of each category of ship.
In this case picking one of these 3:
Achilles 1850 / 600 4 gun, 0 bay, 8 PD
Avalon 1100 / 450 3 gun, 1 bay, 7 PD
Resolute 800 / 450 2 gun, 2 bay, 6 PD
However, something wierd happens here! Instead of the above, the top 3 choices are:
Liberator AGAIN! 1000 / 500 4 gun, 1 bay, 7 PD.
Resolute 800 / 450 2 gun, 2 bay, 6 PD
RAVEN!?! 1600 / 400 2 gun, 0 bay, 6 PD.
What the heck?!?
Hence, the obvious choice is the Liberator as the strongest sidekick (since it is actually a Tier 1, even though a bit too weak).
Otherwise the player takes the Resolute if they really want to trade 2 turrets and some armor/shield for that 1 extra fighter bay.
Even if the Raven's armor is tempting, its extra speed is totally wasted as a sidekick and it is a whole tier removed.
Therefore, the suggestion is to tweak the balance of ships with this new paradyme in mind, focusing on the categories of ships which probably makes more sense in the long run.
Obviously, there is lots of room to work with to make other desirable options within any Tier:
A bigger "Raven" could be made with 3 guns, 9 PD with very heavy armor and shields with high speed meant for outmanuevering. This would allow the actual Raven to be used as a sidekick for a high-speed ship fleet.
A 5 gun, 1 bay Behemeth with weaker armor relative to the Armada could be made, but the bay can only hold Bolter Fighters. Or it gets a 6th slot that is only for Utility (repair,shield boost, teleport,etc).
and so on.