First off I'd like to say that I really enjoyed this article. This approach to deckbuilding is certainly a useful method. The last two week's articles have been excellent, keep it up.
Wait 'til next week

Anyway, as far as methodology goes, I would like to raise one small concern:
In building the final list, you assembled multiple iterations of the Tezzeret deck that would be well suited to particular matchups. From there you complied a composite list of shared cards, and then went on from there to fill out the final slots.
While in theory this seems like an empirically sound method, I'm left wondering whether this actually detracts from the strength of the deck overall, even in the matchups that were considered in the deckbuilding process.
You are exactly right. This is the weakness of my approach. Internal synergies are given less of a priority than external synergies - that is, maximizing each cards effectiveness against expected opponents -- than is typically the case. However, that doesn't mean that internal synergies aren't important or important to my approach. My appoach is just more balanced.
Here's how my approach maintains high level of internal synergy. First, a good number of the cards are present in all potential lists. These cards are the 'core' of the list, since they appear in almost every version of the strategy. They tend to reflect the strongest internal synergies, ensuring that most of the synergies that would appear in any list are present. Secondly, there are decisions to be made in many steps, including decisions in the final step. These decisions can be made with a recognition of possible internal synergy, as I did in the final step.
But really, you have posed a higher order level question, of which there is no clear answer. I have presented this methodology as a counterpoint to the all to common method of building decks exclusively or in too large of a measure based on internal synergies.
It's a higher order question: what is the process of building a deck? And, at a higher level, how do you evaluate what the best process for building a deck is?
I wrote an article a few weeks ago on Legacy, where I built a Grid of one of hte Legacy SCG $5ks that had showed almost every match played in the tournament. The results were striking. Zoo always beat Goblins. Ad Nauseam always Beat Zoo. Zoo always beat Merforlk. And so on.
This caused a number of deep questions on the Source: given this knowledge, is it worth it to even try to win these matchups? It appears not to matter how skillful you are. You just can't win those matchups. But if you try to win them, how? Do you try to mangle your mainboard to win them? Or do you build your sb to do so? Or do you just sacrifice those matchups?
The truth is that there is no clear answer. These are the highest order questions that can just about be asked, and the most difficult, but interesting, to discuss.
EDIT:
From the Source:
So here's a question: assume that, as the article states and defends, Legacy is highly matchup-dependent. What does this imply for how we build decks?
Consider these proposals:
A. Sideboards should be very focused on using hate to remove your worst matchups. You can't afford to make your fifteen from 3 cards against each of 5 decks. Players should pack 6+ cards for their worst two matchups, and maybe some general utility in the remainder. 43land should play lots and lots of combo hate, and fight "fair" against CounterTop.
B. Players should ignore their bad matchups as unwinnable by any sideboarding means. Construct your sideboard to gain an edge in your winnable matchups: 43land should just assume it's never going to face Belcher, and pack its sideboard with tools to fight CounterTop decks.
1. Which of the above is true, if either?
2. Are these statements necessarily contradictory? (perhaps A is true for the best players, who can win their not-terrible-matchups through skill, and B is true for mediocre players)
3. Does the choice of strategy A vs. strategy B differ based on decktype? If so, how do you make that choice for each of the format's best decks?
http://www.mtgthesource.com/forums/showthread.php?p=401444#post401444