I like Skill Challenges.
I don't just like the concept, and sure I've been party to some skill challenges that didn't run as smoothly or realistically as I might have liked - and the same can be said of combats and encounters not based on skill challenges - I just really think skill challenges are cool. That's as-is. I probably wouldn't look askance at any changes made to the basic guidelines (as I don't at the ones they've already made), but I like what's out there. At some point I'll go more into why, but I wanted my first post to make this clear right up front.
D&D's not the only game to use skill challenges as a way to make the game more interesting. They're the only one to call them that, as far as I know, but other games have used a very similar system. Am I speaking of Call of Cthulhu? GURPS? Traveller? No.
I'm speaking of Splinter Cell.
Now, I haven't followed the series into its latest incarnations, and I don't think I ever finished Pandora Tomorrow, but bear with me. In the games, you play a special operations soldier trained to infiltrate and "exfiltrate" hostile areas. The areas are usually filled with enemy guards, sensors, and traps. The "skill" part is avoiding all those. The "challenge" part is that you only have a certain number of chances to avoid them before Bad Things start to occur. Often, this number is three, but it can vary.
Now, sometimes setting off too many alarms, alerting too many guards, or allowing too many signs of your passage to be detected will result in the level ending - or your character being shot - and you having to start over. This is a video game we're talking about, so such penalties are acceptable and more or less expected. Sometimes, you're allowed to make any number of mistakes (apart from outright exposure to armed enemies), but doing so makes the game more "interesting." This is what a good D&D skill challenge should strive to do - not halt the game, but keep it moving with a twist.
For example, in one level of Splinter Cell, every time you trigger an alarm (i.e. fail a skill check) the guards in the level move to a higher state of alert. First they're on the look-out, meaning they're harder to avoid and they're ready to shoot. Then they put on helmets which makes a one-shot kill harder, and raises the odds that a direct confrontation (made more likely by the first failure) will result in injury and more alarms. Finally, they put on body armor, meaning you'll have a very hard time dropping them should the need arise.
This would be very easy to emulate with the Skill Challenge guidelines in the DMG. Stealth, Perception, Athletics, and Acrobatics would allow the party to move around the scene without alerting the enemies (who might not themselves be able to kill the party, but would be a drain on their resources). A failure means that subsequent rolls become more difficult (probably a -2 penalty each time), as the guards are more alert and the easy paths become blocked.
What if this skill challenge ends in defeat? I'll admit that coming up with interesting results for both victory and defeat in a skill challenge is the trickiest part of it for me - as befits its importance. In Splinter Cell, defeat increases the chances of a direct confrontation and death, or depleted supplies for the final part of the level, possibly resulting in... death. In D&D eventual confrontation is expected and typically not as lopsided as in Splinter Cell. Still, there are ways to make it more difficult, and I think that's what defeat in this challenge would lead to. The party would find their enemy ready for them, their objective surrounded by guards and wards. Perhaps they are successful in their objective, a fine default for any skill challege, but their lack of finesse has cause trouble for their patron, or forced the enemy's hand and now there's a new and interesting problem to deal with, rather than the expected next part of their adventure.
What's my point after all this? Skill challenges make the game more interesting, without (directly) bringing it to a halt. Use them for that, design them to do that, and keep Splinter Cell (or Thief, which used a similar technique even earlier) in mind as a basis for your challenges.