Very good article, we may not agree on everything (some people may not agree on anything of it) but we owe to Sulla the effort of starting a discussion about how the best Civ should be.

His effort and example deserve an appropriate reply.
First, I like the basic concept of the design of New Civ: get the feeling of leading an empire without having to micromanage towns and single units.
Moo was extremely good at that, with an interface that simple and intuitive but powerful at the same time.
I have to admit I was an avid player of MOO and sometime I find myself re-playing it.
However very few other games were able to give that sense of being the leader of an empire.
Long story made short: I agree with Sulla on the "Overall Design Goals" and the "Units and Combat" chapters.
It's important to notice that the unit management in this case makes completely sense only if you have tactical combat.
Having 100's of small units and a good automatic system to stack them (see MOO) it's the design that most fits an empire building game.
In pre-history you have a few men roaming the land, until thousands of years later you have huge armies with imposing technology to fight huge wars for the scarse resources.
MOO had a good solution for the production and automatic staking of this large number of units (well described in Sulla's article).
But there are two points that I did not like in MOO and those are still reflected in Sulla's design, even if addressed:
The first point is that tactical combat can be tedious, so a good auto-resolver that brings fair combat results is a must to have.
If we do have it, then tactical combat is not an issue: you use it when you feel it, when you want to feel the "power" of smashing enemy's armies with your hands, and when you need all your cunning to win a desperate battle.
The second point is about the staking in tactical combat: in MOO it was not possible to divide the stacks.
For example if a battle you had 100 units of one type, you could not divide them in two groups of 50.
Being able to divide the stacks in the tactical map could be very important... Imagine having 100 knight, you may really want to divide them in two groups to be the wings of your army.
The concept of "accuracy" is rather good, but it assume that the attacker always strike first.
Units may have another property called "initiative": when one unit attacks another, the first to strike is the one with the higher initiative.
You may have weak units with high initiative (e.g. light cavalry) and powerful units with low initiative (e.g. heavy pikemen)... something similar was archived with 1st strike in Civ4 but the concept I described really comes from Panzer General.
Something that is not described, but only implied, is that in Sulla's design the units are fixed (like in all the Civ serie).
In MOO and in SMAC you didn't have fix models for the units but you were building their design from different categories.
I loved the system in both MOO and SMAC, I wouldn't mind to see it again in a Civ game: you build the design of your units with Attack, Defence, Movement elements taken from what your research offers.
The more "stuff" you put in the design the more the unit will cost.
The MOO-SMAC design of units was a nice touch, but maybe not really fit for a game with historical flavour, but it makes every game slightly different due to the different design that you and the AI can have.
This opens the door for a lot of interesting choices during the game when creating your designs... especially in MOO you didn't have unlimited number of models of units (I think it was something like a maximum of 6 at every each time).
This forced the player to carefully choose the designs, and what to scrap to build a new one.
Hmmm... I'm getting pretty long in my reply I need to shorten it.
About research, I liked the MOO model, and the visibility added by Sulla makes it even better. (short enough I think)
About Civics/Social Policies, again I have to take inspiration from one of my favorite game: SMAC.
In SMAC you always had interesting choices with your policies: you had bonus and malus for each of them.
For example "Planned Economy" gave +2 Growth and +1 Industry but at the costs of -2 Efficiency.
Some leaders were spared by the negative effects of specific policies, leading the player to a very custom game-style with each leader.