This is, imo, a very good thread-idea, as it should give us all some further insight how we and others actually built decks. Sweet

While creating new decks, do we use the skeleton of known decks because it is the best choice, or because we know these
skeletons, have them ready/pimped in our deckboxes and are just used to using them?
Well, quite simply, I use skeletons when decks obviously cry for a special theme (control, speed-combo, etc). There are just cards that have proven to be so very powerful that no deck of the fitting type should be played without them. They are, as Tristal said, simply good cards (in that kind of deck). At this moment, some skeletons of cards I use are:
Control
4 FoW
4 Mana Drain
4 Brainstorm
1 Ancestral
1 Time Walk
SpeedCombo
4 Dark Ritual
7 SoLoMox
1 Crypt
1 Vault
1 Petal
1 Demonic Tutor
1 Yaggies Will
1 Necro
Artifact-based
4 Workshop
8SoLoMoxCrypt
4 Goblin Welder
1 Tinker
1 Memory Jar
1 Ancestral Recall
4 Trinisphere (I know some people do play without them. I wouldn't. A bonus 10-15% 1st turn wins are to good to pass up, imo)
Is it that new decks start with a known skeleton, but after an idea is found "promising" it starts to live a life of its own, generating its own specs?
Most cards will usually be tried first in existing skeletons, with two possible outcomes.
1.
If they work in that kind of deck, they will often be used without thinking about innovation, stifling it. A good example for this is Dragon, which was originally modeled with the basic speed-combo skeleton in mind.
Not until the restriction of Entomb did players try to find a different way to make it work (the Canadians, if I remember correctly). This is where the "skeletons" disrupted innovation. Only after the known didn't work any more, a new "spec" was created, Bazaar + Squee if you want to discard lots of cards per game. And this one is far superior in Dragon than the "known" one ever was, imo.
2.
If they do not work in an existing skeleton, they will either sink into oblivion until some good use for them is printed/surfaces later on ((the usual thing, for example Stax was playable forever before it finally got built and played by more than 1-2 players)
or someone is actually creative enough to see what kind of interactions are needed to make them playable (very rare, Storm + LED for Long.dec is an example, because Storm was broken ASAP)
Or is it that a deck that has a lot of specs of its own when it is introduced gets old specs forced upon it by people thinking they already know the deck before ever playing it (in other words, only the "bad" players try to hang onto specs, while the "good" ones try to invent new ones)?
Both good and bad players use specs. The good ones realize which spec to try for which kind of cards* and also realize when there is no working spec for a new card in existince.
After trying existing specs, good players will go over to think about new specs that might work better (or at all, if there is no existing one). Those are really hard to find, considering how powerful T1s specs actually are.
*There might be multiple plausible specs. A good example is WorkshopSlaver vs Control Slaver.
I think you are confirming the reason for my question. You say any blue based control should include the cards you mentioned. However, the old 4 gush GAT had next to none mana sinks in the deck for mana drains, being the reason a lot of people played regular counterspells instead of drains, but still there where lot of lists using drain. That in itself was because people think "mana drain is superior to counterspell". That may be true in most cases, but not always (everybody burning to death because of drain mana will know what I mean).
GAT had quite a few mana sinks and the brokeness you could reliably start with Drain-mana was enough to actually play the Drains (at least I rarely burned from them in testing). GAT was a brokeness-deck, and as such playing C-Spell over Drain was simply wrong, imo. It had nothing to do with a wrong idea of Drain being superior, it actually IS superior as long as you have more than around 5-8 spells that cost colorless mana.
I think Gifts Ungiven decks are an interesting starting point for this idea because of how self-contained the kill can be. You have your 3-4 Gifts Ungiven and maybe 10 possible cards to search out (which is also including cards that would in all likelihood be in your deck anyway, like Lotus and Will,) so now you have 40+ slots to fill up with well, anything.
I was thinking the same thing. Gifts seems a card that is made to be broken. I was thinking how easy it would be to get a Slaver lock with Gifts.
Just using a pretty basic build you could conceivably get a lock quite consistently and early using efficient search to get Welder/Reanimate/ Artifact combinations. Something along these lines could generate a new arch type based on an existing skeleton. I haven't put enough thought into this yet but in my highlander deck I've been using the Gifts/Reanimate/Welder/Bringer combo already and each time it resolved I've ended up winning the game. I've been testing three Gifts/three Reanimate builds for about two weeks now looking for the best build.
Well even though Gifts is rather open-ended, imo there are some basic things that can be used as pointers for Gifts to find a basic skeleton to use.
Speedcombo won't use it, because there 4 mana is to much for a regular business-spell, if you can get Draw7s at 3 and just want to kill ASAP.
Pure control would be transformed into combo-control simply by Gifts nature. I just screams combo-kill.
Aggro (and aggro-hybrid-decks)... well, I'd rather not use cc4-Instants in something meant to beat down as hard and fast as possible.
This leaves us with Combo-Control. There we have two skeletons to start from, COMBO-Control (like TPS) and combo-CONTROL (like Tog or Slaver).
CAB has versions derived from both starting points. The TPS-style decklist (designed in cooperation with Michael Heiduk) is, in our opinion, not able to abuse the maximum 4 Gifts sufficiently due to the high CC of Gifts. We currently use only 2, if you get to the point where you cast them, they usually win the game here, too.
As for Combo-CONTROL, the heavy disruption Tog-style approach is Gifted, as already published. I also have a GiftSlaver (untested) version, modeled after Control-Slaver, which looks promising on paper. I just think the heavy disruption-approach more fitting than the pure-power approach of Welder, because Gifts alone already produces so much power, so that's what I tuned first. This is next in my "decks to test" line, though. I might put the build up somewhere on the drain by next week, when I have at least some testing with it.
Another point of view is the subject of the Gifted. The Gifted might just as well be a combobuild trying to abuse Gifts Ungiven. However, the Germans are "known to be fond of 4CC", so they build a 4CC like deck abusing Gifts Ungiven. This isn't necessarily bad, but maybe a combobuild is better. But instead of starting of with a blank slate and start of with 4 gifts ungiven, they probably started a list with 4 FoW, 4 Drain, 4 Gifts, etc because they are used to 4CC.
Actually no. See further down.
Actually, Mons shoved them into a mana severance/belcher deck that had been played with some success. I don't think it had anything to do with Mons love for 4cc but rather a desire to protect his win condition that dictaed the use of counters. I think he also did not want to be beat by an early Trini.
Actually, our thoughts went like this:
a) We knew we had a spell that was completely insane for setting up Yawgmoth's Will.
b) A cc 4 instant is far to expensive to be used in speed-combo (see the answer a bit further up).
c) Mana Drain + 3 colorless mana in the cc = tech
d) Gifts sucks your library empty of good cards rather fast. So the final Will just HAS to resolve -> heavy disruption. The alternative is playing multiple Will-style cards (aka Welders).
All this called for a Tog/Shining style skeleton for the deck, pretty much like bebe says in his second-to-last sentence. We didn't start with "oh look, a new carddrawer, let's build a new keeper", we looked at Gifts specifications and built the deck accordingly. I would be VERY surprised if s.o. actually finds a non-controlish deck than can abuse Gifts sufficiently. 4 mana is just to much for anything without heavy disruption and I'll go as far as saying 4 Gifts should always be acompanied by 4 Mana Drain because of their natural synergies. For early winning, 3 mana draw 7s are just better than 4 mana double Demonic Tutor + double Entombs. .
Btw, Mana Severance-Belcher was just the best 2-card-kill-combo we found, we didn't model after any kind of Severance-Belcher deck. I don't even know of any non-monoU deck that used it successfully. As mentioned in the article, that kill later proved superflous, though.
And @bebe: it's Mon, no s. I'm not a personal friend of Richard Garfield ;p