FYI if you go into the unit files and just edit the bowmen's collateral damage stats down to 0 the AI doesn't use archery barrage anymore.
You might want to look into giving more of the future units some degree of fluff text and whatnot, like the Assault 'Mechs and similar. Also nice (sometime in the future anyways) would be modifying the civs to have a unique unit in each era-classical, medieval, renaissance, modern, and future.
Some bugs you might want to fix though:
1. Quests like "The Best Defense" which require a specific building don't accept the unique equivalent. I'm pretty sure about that although I could have just miscounted the numbers of Towers of Davids I built. If they don't accept the unique equivalent it'd be nice if they could be made to. If they do, that could be made far more clear.
2. Upgrade logic is weird. Clones are better than workers but you don't have the ability to replace your workers with clones, etc. It'd be nice if you could.
3. Special Operations Command doesn't actually do anything, since you can build SF without it. It's kinda 'eh' if all it did was unlock special forces, too.
4. Fieldsman I/II/III are rather pointless since I believe in every circumstance Combat X is better (combat has similar +defense in open fields but no penalties to hill and forest defense).
5. Firaxis HQ doesn't produce Hit Games despite its description. It really should.
6. The Secret Army Base can be built by a general way, way before the techs come up. I think I had one in 4800 or so BC.
7. The Garrison doesn't give XP to mounted units despite it being available at about that time. Similarly the meeting hall isn't obsoleted despite not giving XP to any non-recon modern unit. A suggestion to fix these is to not obsolete the barracks and return it to just giving 2 XP to ground units, and having the garrison cumulative over it (+1 XP? +2? Doesn't matter too much.) The meeting hall should be obsoleted instead, as formalized training becomes the norm instead of lore passed down.
8. Emancipation and Contracting are not mutually compatible. I suggest trying to fix it so that you take the happiness penalty if you're not running one of those two.
If you're taking suggestions:
I'd make the bioenhancement center just give a free promotion instead of XP. a "Cyborg" promotion that adds +10% strength (just like Combat I) would let that work without any issues with conflicting with aggressive/protective. Oh yeah, and as a Alpha Centauri reference you totally need the Cyborg Factory (bioenhancement center in every base).
Change Special Operations Command to "Urban Warfare Center" and have it give a "Urban Warfare" promotion that adds to city attack and defense for units built in that city.
The use of a Bleeder graphic for a supersoldier is something I don't terribly like. If I had my way I'd have Homo Superior give a +strength bonus for all units (+5%? Something small but noticeable), to represent your awesome superhumans in every level of everything. Or rename the tech to "Posthumanism" and make "Homo Superior" a wonder that makes specialists better.
Find another graphic for the fusion tank. It actually looks more primitive than the other future units. Similarly the high-tech infantry should get their gun graphic replaced, that giant tube looks jarring. I understand you probably aren't doing all the modeling yourself, but I'm sure you can find a 3D modeler who will help with that.
Black Ops. Like ground-bound privateers. Just give them "cannot capture cities" and make them units with hidden nationality. They could come alongside special forces or replace special forces at a later date. An early equivalent could be called an "Assassin".
Combat Engineers would be cool for cities that are near to the front lines as an alternative to workers in the modern age. Like the unique worker with the ability to defend themselves combat engineers would be more expensive but have a defense strength of 20 or so, enough to hurt an attacking modern infantry unit.
Black Helicopters. On a more serious note, some sort of stealth transport that can cross water.
Wonder suggestions: "Drexler Assemblers" as a wonder that has the result of +1 hammer to all tiles in the constructing city.
SkyNET. +research and +military unit production.
The GPS Network for +road/railroad movement and +commerce, as well as increasing city bombardment damage by artillery and aircraft (start with accuracy I?)
Orbital Mind Control Satellites, which reduce the chance of a revolt by 50% or so.