When I first read about skill challenges, I felt a lot of excitement about the possibilities - the whole wide world outside of combat got an objective-based XP award! Having the official material in hand and running my first challenge for D&D Worldwide Game Day PHB, I didn't find the experience as fulfilling as I'd hoped. At an established table I'm sure things would have been different for me, but I'm glad I was running a group I was mostly unfamiliar with through a skill challenge. I was better able to decide what I didn't want out of running a skill challenge, and framed some design goals around that. Then I went to work house-ruling, and put together something I like enough to share.
Here's my negatives-based list of design goals, as best I can remember it (this was a long time ago for me);
1: No willy-nilly rolling. Without any kind of initiative structure implied, players either rolled whenever they had an idea, or one leader PC would hammer the same skill over and over. This had the effect of diminishing overall participation.
2: Skill Challenge Init shouldn't look like Combat Init. This is sort of a personal aesthetic thing for me, that I hope also keeps players from entering a combat mentality when I start up a Skill Challenge.
3: Players shouldn't be afraid to participate. With the '3 Strikes' rule in place, some players will only act if it's a sure bet they've got a high skill to roll. If not, they'll pass to someone who does.
4: No Assist Another conga lines. I'm less concerned about the bonuses and more about how dull it can be to line up behind another PC and hope they do their thing. From a DM perspective, it often reduces the number of interesting things players do to entertain me in a round. Sometimes it makes sense and the teamwork is dramatic and interesting. Sometimes it's gaming the system.
After some futzing and searching, here's what I came up with, and what I've been using in my games since; A big thanks to the person who made the Dex Battlewheel, a lovely gaming aid that I've framed lots of fun encounters around!
As you can see, the wheel is divided into 8 tics. Players put their minis down on the board in an order determined by the number of relevant skills. Normally I'll put everyone on a different tic to start with, but the chart illustrates the 'first-in, first-out' rule that I use pretty clearly. Primary Actions take 3 tics and count toward successes, Secondary Actions take 2 tics and provide various bonuses. Reactions are rare and caused by events designed into specific challenges ('On tic 4 the ship rolls nearly on its side! Roll Acrobatics and move 1 tic!').
A player can delay their action to assist someone else or solicit someone else's assistance. Also, some Secondary Skill successes can buy the players more time by adding an extra tic to the end of the round.
The players have the Challenge's Complexity in rounds to gain enough successes to win the encounter. Right now I'm sticking with WotC's number of successes, but I feel comfortable raising the number a little for more difficult encounters. As it is, if players roll nothing but Primary Actions, they have 8 chances to get 4 successes in one round for a Complexity 1 Challenge. Plenty of reason to be less fearful about standing up and doing something when it's your turn, and I'm less fearful about planning in some curveballs and secondary goals to heighten the tension.
I've been running this for about 6 months and having a great time with it!