This one is short and sweet.
Firstly, mid- and end- rank ships should be comparable in terms of power. As it stands now the end rank ships are always a better choice unless you really want the class role of the mid tier. For example, there is no advantage to flying a Steel Harpy (Rank 5 - the “middle” of Tier 2) once you’ve unlocked the Hydra (Rank 6 - the “end” of Tier 2). My suggestion would be that both of these ships would, if the current ship tree remained unchanged, be equally good.
Now for the meat of my suggestion…
Each tier (except tier 1, which would work a little differently) would be laid out as follows:
Entry rank (4, 7 and/or 10) would contain three ships - the default Interceptor, Fighter and Frigate of each faction.
Mid rank (5, 8 and 11) would contain the three upgraded defaults.
End rank (6, 9 and 12) would contain the three alternates.
What is the point of this you ask? Well, the simple answer is that it gives each faction’s “best” ships faster, with the secondaries being a reward for persistance, without necessarily making them the ‘best’ ships to go for. It also helps cement the roles of the factions. For example…
Let’s assume, for sake of argument, that the best Tier 2 Command Fighters in this revised layout are the Jericho’s “Machete Type S” and the Empire’s “Phobos Aura”. If you play Jericho you unlock the Machete Type S at Rank 5, whereas the Phobos is at Rank 6. This means if you want to fly a Command Fighter you benefit from flying Jericho - you get the ship faster and can begin leveling synergy sooner than if you tried the Empire route. However, both ships would be an equally ‘good’ choice - the Phobos would not be better just through being one rank higher.
As my example hints, the ship tree needs to be moved closer to the pre 0.8.0 version for this to work, but I think it would be worth it overall.