I'm posting this as a process oriented guide. The (now formalized-ish) process I stumbled on and created through the course of this story was very useful to me and is a tool I will use in deck design going forward. Hopefully others will find the process helpful/useful as well. If you see a flaw in the process or can recommend an improvement, please do so.
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I've been working on the M11/Mystical Tutor ban update to my pet Slide deck, and everything I did seemed to be making the deck, if not worse, then at least not better. If anything, the lists I was ending up with were having less success vs. everything that the ones I started out with. Given that, I decided to go back to the beginning, and completely redesign the deck from the ground up. I started by listing all the cards I wanted to include both maindeck and sideboard. This totaled out to way more than 75, and I wasn't really sure what to keep/cut. So, in a fit of inspiration, I decided to "chart" the metagame into sections and list what plans/strategies/cards were good vs. each sector, and then go from there. This is what I came up with for metagame sectors, any deck not specifically listed should be reasonably obvious where it goes, also, several decks cross classification lines, I tried to put them where they fit best based on commonalities and overall gameplan. For a card to be considered "good against" it has to specifically and meaningfully mess with the opposing decks' gameplan. Swords is useful vs. any deck with a creature or manland, but its not "good against" all of those. Similarly, Inquisition of Kozilek is useful vs. any deck with cards cmc < 3, but it's not "good against" all of those either.

Dark Ritual Decks: ANT, TES, Solidarity, Belcher
Commonalities: Play lots of spells in one turn. Resilient to disruption, win via combo/all in spell.
Cards good against: Inquisition of Kozilek, Orim's Chant, Gaddock Teeg, Ethersworn Canonist, Leyline of Sanctity.

Graveyard Decks: Dredge, Loam, Lands
Commonalities: Utilize graveyard to create massive virtual CA and quickly overwhelming board presence.
Cards good against: Tormod's Crypt, Extirpate, Bojuka Bog, Life from the Loam, The Tabernacle at Pendrell Vale, Crop Rotation.

Vial Decks: Death and Taxes, Goblins, Merfolk
Commonalities: Lots of little guys entering play free or undercosted, lots of pump, lots of draw, usually some LD elements.
Cards good against: Swords to Plowshares, Maze of Ith, The Tabernacle at Pendrell Vale, Ghostly Prison, Pernicious Deed, Akroma's Vengeance, Basic Lands.

Bolt Decks: Zoo, Burn, Red Deck Wins, Cat/Goyf Sligh
Commonalities: Beat with big undercosted creatures early, finish with burn to the face.
Cards good against: Swords to Plowshares, Kitchen Finks, Obstinate Baloth, Leyline of Sanctity, Basic Lands.

Counterbalance Decks: Landstill, Jace2.dec, Thopter
Commonalities: Establish various softlocks backed up by counterspells, many non-creature permanents.
Cards good against: Krosan Grip, Pernicious Deed, Extirpate, Gaddock Teeg, Raven's Crime, Wasteland, Qasali Pridemage.

FOW Decks: Threshold, Thrash, New Horizons, Fairy Stompy
Commonalities: Small number of big guys attacking backed up by free countermagic w/mana denial.
Cards good against: Pernicious Deed, Swords to Plowshares, Life from the Loam, Bojuka Bog, Crop Rotation, Basic Lands.

Prison Decks: Stax, Enchantress, Dragon Stompy
Commonalities: Establish hard locks on the game through massive permanent advantage.
Cards good against: Krosan Grip, Qasali Pridemage, Akroma's Vengeance, Gaddock Teeg, Pernicious Deed, Basic Lands.


Cards in multiple categories:
Gaddock Teeg, Swords to Plowshares, Crop Rotation, Bojuka Bog, Basic Lands, Pernicious Deed, Krosan Grip, Leyline of Sanctity, Qasali Pridemage, Akroma's Vengeance.


Combining the above cards was a nice starting point, but didn't really give me a useful deck. After compiling this list, I realized I wasn't going to just need specific cards to deal with each of these sectors, I was going to need a plan of action that addressed the decks' core strategy and provided me an achievable path to victory. So I redid my matrix like this:

Dark Ritual Decks: Prevent casting of key spells. - Gaddock Teeg, Orim's Chant, Leyline of Sanctity.

Graveyard Decks: Eliminate established graveyard, eliminate key engine cards. - Crop Rotation, Bojuka Bog, Extirpate.

Vial Decks: Repeatable way to kill small - medium creatures. - Sorin Markov, Witness/Slide/Swords, Gideon Jura, Preacher, Diamond Valley.

Bolt Decks: Lock down burn spells, repeatedly gain life while preventing attacks/burn. - Sorin Markov, Elspeth Knight Errant, Gideon Jura, Leyline of Sanctity, Diamond Valley.

Counterbalance Decks: Destroy large numbers of artifacts and enchantments, eliminate recursion. - Pernicious Deed, Akroma's Vengeance, Qasali Pridemage, Krosan Grip, Extirpate, Bojuka Bog.

FOW Decks: Secure manabase, kill and shrink threats. - Basic Lands, Crop Rotation, Life from the Loam, Swords to Plowshares, Gideon Jura, Bojuka Bog, Pernicious Deed, Preacher.

Prison Decks: Secure manabase, destroy/prevent large number of artifacts and enchantments. - Basic Lands, Gaddock Teeg, Qasali Pridemage, Pernicious Deed, Akroma's Vengeance, Krosan Grip.

After all of that, I ended up with a deck that was pretty close to finished, and was able to go directly to the playtesting/tweaking phase, where results so far have been positive. This method of deck construction has also been very helpful in determining how to sideboard, since I have a much better idea what I'm going to do vs. a specific deck or strategy, and I have a clearly visualized path to victory.

Sometimes the analysis of decks as a sector can lead to new insights. For example, I realized that mass removal really isn't that great vs. the vial decks because they all just reload on creatures so quickly that what you really want is a way to kill one or two dudes every turn, rather than wipe the board just to watch it get immediately refilled. This in turn led to my decision to run critter kill 'walkers in conjunction to the old Preacher/Valley tech which is in addition to the recur StP every turn plan. The redundancy of effect makes it unlikely that they will be able to prevent at least one of these options from materializing, thus making it more likely that I can in fact successfully execute my chosen plan.

I know some of this may seem redundant or obvious, and I suppose it is, but I know that I often put together a deck and then playtest it and realize, oh crap, I'm weak to X, so I'll throw some Z into my board because its good against X. etc. etc. This seems a more formal, organized, and useful way to create a deck, or to tune one, to an expected metagame. "The Process" in short is:

1) Divide metagame into sectors of similarity.
2) Figure out which of your cards are good vs. various sectors.
3) Develop a plan based around those cards to deal with each sector.
4) Build your deck in such a way that it can execute required plans.

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Like I said at the beginning, hopefully this is helpful, and I'm more than open to suggestions on improvements, thanks.