colored in cubes is just an example of what a player might have unlocked 
3x3 and 3x2 clusters are the actual ship choices
3x3 for main roles in that faction
3x2 for minor roles in that faction
The more advanced the ship is, the more slots it has BUT
Base attribute is reduced to compensate
Different variations give different passive bonuses
this is what i actually expected as i started this game, because my T1 weapon had more DPS than my T2. I was pretty disappointed to find out, that the higher the tier goes, the more the stats grow in every direction, including implants. It is partly why I like T3, since with all the golden ship variations available, T3 endgame almost feels a bit tier-less, any R8-R9 ship has some value but also some weakness.
I got used to the ship model we have atm. very much, but I would still like this kind of shiptree.
However you did not touch the modules - which are also tiered. Higher tiered ships would have higher tiered modules giving better bonuses or more variation in fitting with the current module-model, it might even work.
I like your drawings. But your player obviously hates Fed Recons…
If I had to balance that ship tree I would
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Decide on slots distribution for Expert Ship which has the most slots
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Then stick ‘benchmark’ modules on
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Resulting attributes becomes Basic Ship stats
In essence, game designer will equip Basic Ships for you so the player doesn’t have to worry about it. If they wanted different they have to unlock the advanced models and customize. Doing it in reverse will help keep the different models at relatively equal strength. This also means there are no tiered modules since everything now belongs within that same powerband.
How the grind looks like for modules I don’t particularly care so much. I’m only against the fact that current ones have different grades and that is anti-competitive. But to keep things consistent, module unlock works better if the ‘benchmark’ modules serve as the starting point. All other modules that may fit into a slot then branches off from the starting benchmark module.
example:
Expert Fed Gunship has
1 Engine
1 Capacitor
2 Shields
2 Hulls
1 CPU
Benchmark Engine mod is Catalyst Injector (raise max speed +5%)
So Expert Model base speed is 380m/s
Basic Ship max speed is 400m/s
Tiered modules cannot exist in this ship tree as that will break Basic Ship stats.
You could keep the ‘advanced’ modules like Auxiliary Generator (raise max speed, penalty AB energy use) as that still works.
Infact there should be more of them. In the example above, Expert ships can exceed Basic Ship max speed but there is a trade off.
To make up for less grind with modules (since there are no multiple grades and tiers) you could limit mods to specific model levels
example
Basic Ship only has main weapon slot.
Starter gun depends on faction
To use other guns you need to grind and unlock them
Guns unlocked at Basic level ships can only be used on the Basic ship itself and its’ variants
When you unlock the ship’s Advanced level you only have access to a starter gun and need to repeat the grind again in order to use other weapon types.
Same thing when you unlock Expert level ships. Grind again to unlock the modules.
Isn’t as bad as it sounds. Depends on slot distribution at each level. I would say
Basic = Weapon, Missile
Advanced = Weapon, Missile, [Engine / Shield / Hull] (Varies depending on role and faction) eg. Jericho ECM = Engine+Shield but Empire ECM = Engine+Hull
Expert = Weapon, Missile, Engine, Capacitor, Shield, Hull, CPU
Not that many to unlock. And cost of unlocking can be adjusted.
There should also be new specialist modules to further set ships apart and give them niche functionalities to keep things interesting.
Probably more Class limited and Role limited passive modules that isn’t ship attribute related. eg. CPU module that can decloak enemies within range. Or Capacitor module that can cancel negative buffs on one ally within range every 50 seconds. Or hull module granting immunity to drones when shield is down. Engine module that cancels the first lockon when a second lockon is made against the ship once every 35 seconds. Shield mod that cancels critical hits when Shield is less than 50%.
Me likes this idea. +1.
Grind to specialize, with the option to stop whenever you feel comfortable with your level of specialization.