Odd, but my impression of Alpha Centauri was a very different one than that of Alexander. I also think that the improvements he suggests are not very high on my list.
When I first saw Alpha Centauri, my immediate reaction was: Wooh, this is just a better Sci. Fi. Civ. I like it anyways, 'cause I like everything that looks like Civ. Only over time, I realized how much more depth the game offered.
You got Advancements, same as in Civ, and the Secret Projects are just another fancy (yet inappropriate: your secret projects are the least secret thing about what you are doing) name for a wonder. No big change there.
Deleting obsolote units is made much easier by the newer patches: It takes two clicks/unit. No biggie, if you custom design only the units you need, rather than letting the computer do it for you.
Different ship classes: You have two different chassis, which made for a multitude of different ships. Everything from destroyers (big gun, no defence) over escorts (all defence+AAA) and transports and carriers to all around battleships. Yes, you have subs, you just need to stick a special ability on your ships. Too bad the AI sees them anyways.
Names: Too much small scale battle focus. I want to build an empire and focus on strategy. Naming individual units makes the single unit seem too important. WHat comes next, naming my rec commons or network node?
SPecial Elite units: They already get a movement bonus and an attack/defense bonus of +50%. Also, you can upgrade them. Everything Alexander asks for.
Grouping/stacking units: YesYesYes. The one thing AC needs and CTP has.

I'd like to see that very much.
Double faction leaders: The developers have gone through a great deal of effort to characterize the different leader personalities and enhance the athmosphere and story. More personalities take that depth away. If you really don't like the pix, you can edit them easily anyways.
newspapers: They have the interludes, which are much more athmospheric than most newspaper coverage which I have seen on other strategic games. And they have neato SP movies. Not to mention that it's kinda boring to read the same old
Glorious victory for University shard chopper in a close battle against a Spartan terraformer' headline for the 100th time.
Battle details: It lists the different mods and does the math for you. That's pretty cool and that's all I need. I can see how the battle is going in the big picture myself, and I can always check the overall unit stats of each faction. Though it would've been nice to see the losses split up in losses against different factions.
I think the author overlooked the possibilities of probe teams quite a bit:
They can plant genetic engineered viruses into cities. They can assassinate researchers. They can ´turn units around.
Going too much into detail there and develop different kinds of disases would lose once again focus on the strategy. You have nervegas. PB's are devastating enough as it is, no need for additional damage, IMO. I think those three options and the advantage it gives when using them is all that I need to explore the depth of atrocities.
I think naming people, even commanders, and doing assassinations of specific people goes again too much into micro-management. A militairy unit is the smallest representation I want to deal with. I don't want to manage the life of every single citizen.
I agree that the whole idea of 'space travel' should've been expanded. Even though we start ahead in the future, Civ:CTP has a much nicer focus on space building. Floating cities and space exploration are just two ideas.
So the only two improvements I agree with Alexander on are basicly the two aspects I like about Civ:CTP (unit stacking & space building). Otherwise, I wish they would improve the AI quite a bit. There's tons of room for improvement there and I don't think all of it would be hard to implement.
-joer.