So why exactly do you find it weird?
What I find weird is that, if Mearls and Baker write a skill challenge in which a consequence is a change in recovery time, that is (presumably) permissible within the rules; and if WotC publishes disease and curse rules which have, as one component, that recovery time for healing surges or powers is delayed, that is (presumably) permissible within the rules; but that if I implement such a consequence then I'm disregarding the action resolution mechanics!
What mechanics am I disregarding? Skill challenges, and choices within them, have consequences, including mechanical consequences. One well-known species of mechanical consequence in 4e is delaying or otherwise toying with the recovery time for resources and abilities. I have implemented such a consequence. That's exactly how 4e is intended to play. It's not disregarding the mechanics: it's applying them.
So did your skill challenge have as one of it's "rewards" (and remember you wrote it out earlier) that the DM could activate a player's familiar (without his consent), strip him of it (through said activation, DM fiat of the artifact rules and without the players consent) and change the recharge rate of said resource as a "reward" or "goal" of a "successful" skill challenge???
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Wait so the player activated his familiar? Or did you take control of his resource, activate it so it could take damage and then arbitrarily take it away because he chose not to funnel souls to Vecna... If so, wow... you not only arbitrarily stripped him of the resource, you also took over control of the resource in order to strip it away without his consent...
First, how would you possibly know what my player did or did not consent to? Every post you are making about makes me think that you have no idea about the dynamic of my game.
Second, it's well established in the game that the familiar in question has something of a life of its own. It is a watcher for Levistus. It also recently turned itself invisible and filched a ring for its master (ie the invoker PC). That's part of what the player is looking for in his familiar, and is part of the context within which he implanted the Eye of Vecna into it.
Third, I don't think you have a very good handle on how to run a skill challenge. Suppose the challenge had unfolded like this, instead: I invite the player to make a Perception check, and when he does I tell him that he notices a fire has started, and some MacGuffin is sitting in the middle of the fire. He then makes an Athletics check to have his PC rush in and grab the MacGuffin from the fire before it is burned to a crisp. If I said that the PC suffers level-appropriate fire damage, would you call that "GM fiat" not grounded in the action resolution rules?
Or here is another example, this one not hypothetical but from actual play, when the PCs reforged the dwarven thrower Whelm into the mordenkraad Overwhelm:
I adjudicated it as a complexity 1 (4 before 3) skill challenge. The fighter-cleric had succeeded at Dungeoneering (the closest in 4e to an engineering skill) and Diplomacy (to keep his dwarven artificers at the forge as the temperature and magical energies rise to unprecedented heights). The wizard had succeeded at Arcana (to keep the magical forces in check). But the fighter-cleric failed his Religion check - he was praying to Moradin to help with the process, but it wasn't enough. So he shoved his hands into the forge and held down the hammer with brute strength! (Successful Endurance against a Hard DC.) His hands were burned and scarred, but the dwarven smiths were finally able to grab the hammer head with their tongs, and then beat and pull it into its new shape.
The wizard then healed the dwarf PC with a Remove Affliction (using Fundamental Ice as the material component), and over the course of a few weeks the burns healed. (Had the Endurance check failed, things would have played out much the same, but I'd decided that the character would feel the pang of the burns again whenever he picked up Overwhelm.)
In running this particular challenge, I was the one who called for the Dungeoneering and Diplomacy checks. It was the players who initiated the other checks. In particular, the player of the dwarf PC realised that while his character is not an artificer, he is the toughtest dwarf around. This is what led him to say "I want to stick my hands into the forge and grab Whelm. Can I make an Endurance check for that?" An unexpected manoeuvre!
Are you really saying that it is not permissible, within the rules, to adjudicate that a character who shoves his hands into the forge in order to succeed in a reforging operation needs healing?
Or yet another example from actual play: the PCs negotiated with some duergar slave traders, and with a successful resolution of the skill challenge reached an agreement to redeem the slaves for an agreed sum at an agreed future date. When the PCs then turned up at the appointed date and time, and paid over the money, the slaves were released. Had they not paid the money, the duergar would not have released the slaves for free.
Are you really saying that it is not a permissible consequence of a successful skill challenge that a PC owe an NPC money?
I could multply the examples: a player fails a Diplomacy check, and as a result the key NPC in a fit of anger throws the widget over the cliff to fall into the water below; it is not poised on one final roll required which if it fails will make 3 fails, if it succeeds will make the required number of successes; the player of the thief declares that his/her PC jumps over the cliff after the widget, to catch it before it falls!
It seems to me that the success of the Acrobatics check tells us whether or not the PC caught the widget in mid-air, but s/he is taking damage from the fall either way!
As the rulebooks, say, skill challenges have consequences, both story consequences and concomitant mechanical consequences.