I hope you don't mind my obsession with this, but I am so inspired by this that I hope to use it in my own D&D game, and incorporate it into a game I'm creating, if that's okay with you (it's not going to be published, just made and shared)!
I came up with a few more ideas to extend the versatility of the system. You could have a system similar to the complexity to determine how many checks can be made per action round. 1 is the most difficult, as it means only 1 check can be made per round. It increases from there, and can help determine how many XP the players get in the end.
Also, the complications should come in helpful versions as well. These helpful complications would activate when the DM makes a failure check and it comes up lower than the target number. They can be things like revealing other conflicts, revealing secondary skills available, giving a bonus to skill checks, adding success points to the next round of skill checks, removing failures, rolling twice and using the lower result for the attack, requiring more failures to fail, and more. I also thought of a new negative complication: Detrimental. It's usually last, as Fundamental is usually first, and when a failure occurs in this conflict, it removes successes from all the previous conflicts!
Another idea, though this is a bit of a stretch as it goes against the idea that player's checks don't contribute negatively to the challenge, is negative skills. When you use this skill, you lose previously gained successes in the conflict. You compare your check to the table as normal, but inverse the SPs. So, say you make a check that would normally give you 4 SPs. It turns out to be a negative skills, so instead you lose 1 SPs. Inversing the SPs also inverses where the 0 is. The 0 is at the top now, so you have to count backwards for the SPs: equal to or over the highest number is 0, equal to or higher than 4 SPs is 1 SP, and so on. If you get lower than the lowest target number, you lose 5 SPs in that conflict.
I transformed the Negotiation skill challenge from the DMG into a Conflex skill challenge, to test out some of my ideas. It could work with more testing and tweaking. It uses the assumption that the DM tells the players the goal of each conflict and the primary skills of each conflict (except for Conflict 4, because it has the Unapparent complication, so it isn't revealed until the players are Enlightened of it).
Negotiation with the Duke
The duke sits at the head of his banquet table. Gesturing with a wine glass, he bids you to sit. "I'm told you have news from the borderlands."
Complexity: 3
Conflict 1: We have the same goals.
You must empathize with the duke to encourage his assistance.
Primary Skills: Insight
Secondary Skills: Streetwise
Complications: Fundamental, Enlightening: Conflict 2 (this means that a success causes the DM to tell the players everything about Conflict 2 that they didn't previously know, i.e., that Intimidate is a negative skill. A success refers to the DM rolling a failure check and not meeting the target number).
If you don't understand who you're talking to, you'll eventually realize that you've been getting nowhere when you thought you had progressed.
Conflict 2: Surely you can see the sense of that.
You must entreat the duke for aid in your quest through diplomatic procedures.
Primary Skills: Diplomacy
Negative Skills: Intimidate
Complications: Enligtening: Conflict 4.
The duke refuses to be intimidated by the likes of you.
Conflict 3: It's worse than it seems!
True, the goblins don't plan on attacking the duchy. But the duke doesn't have to know that.
Primary Skills: Bluff
Complications: Precarious, Detrimental.
The duke does not take kind to being lied to.
Conflict 4: History is doomed to be repeated.
Remembering about bloody battles of the past, you can warn the duke not to make the same mistakes as his predecessors.
Primary Skills: History
Complications: Unapparent. Helpful: +2 (this gives a +2 bonus to the next character's skill check).
When the duke reveals that he has participated in battles in the past, someone with knowledge of those battles warns the duke that more bloodshed could be avoided if he gives them aid.
Of course, this is your system, not mine. If what I'm saying goes against the goals you had in mind when designing the system, feel free to ignore me! I am personally looking for a skill challenge system that encourages DMs to give players more options than battle after battle.