Ok, let's get my side of things. First of all, sheepmonster, those are very good unit lines for the chiss and alliance, but let's concentrate on the core mod for now. The beta was good, but I have an idea for a more unified and balanced unit tree for all nations. To some, this may seem that it will take away from each civ's individuality, but we can still offer that in unit stats. So without further ado, my ideas,

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First of all, ranged units.
Blaster trooper 1 > Blaster Trooper 2 > Blaster Trooper 3 > Blaster Trooper 4
This would allow a new regular, offensive unit every era. A Rebel example of this is:
Rebel Trooper > Hoth Soldier > Rebel Commando > Mon Cal trooper
Yuuzhan vong
Thud Bug Warrior > Razor Bug Warrior > Blast Bug Warrior > Yuuzhan Vong Priestess
I haven't figured out defense yet for the singular nations, but I figure that we'll have the one-each-era thing that is in offense. For shuttles, I agree with sheepmonster, 1 is enough. For one-man fighters, I say we have
Fighter > Advanced Fighter > Super Fighter
We have the fighter in era 1, advanced in era 3, and super in era four. Rebels would have it like this:
Z-95 Headhunter > T-65 AC1 X-wing > XJ1 X-wing.
How would we compensate for the lost era? With a new line of fighters!
Fast Fighter > Fast Fighter 2.0 > Fast Fighter 3.0
To be in eras 2,3, and 4 respectively. For the Rebels, it would be:
A-wing > E-wing > Missing link (it would be V-wing, but the Republic is low on space vehicles, so let's give it to them)
The Empire would be:
TIE Droid > TIE Interceptor > TIE Hunter
For jedi/sith/amphistaff warrior, it would be:
Novice > Padawan > Student > Knight > Master
For mechs:
Mech 1 > Mech 2 > Mech 3 > Mech 4
In eras 2,3 and 4. The Empire would have:
TIE Crawler > AT-PT > AT-ST > AT-AT
The Yuuzhan Vong
Acid Walker > Lava Insect > Rakamat > Fire Breather
BTW: there should be a bomber in era 1 and era 3,
Well, that's just me spitballing. Anyone else agree?