If you had to choose between the two for a one way journey, which one is more scenic?

I enjoyed Million Dollar Skyway - very beautiful. Even if one-way - stop at some lookout areas to "look back".

(but I don't believe I was on the San Juan).

The Million Dollar Highway is just the Durango to Ouray portion of the San Juan Skyway loop. Durango to Ouray is more spectacular if you only do half of the loop, but it's nice to drive the whole route.

Clarification: Durango to Silverton to Ouray via 550 is more spectacular than the stretch from Telluride to Dolores to Durango. The entire loop makes for a beautiful drive.

I am a wimp. When I drove from Durango to Silverton I was very nervous in some sections. From there to on to Ouray it's not as scary.

I don't get at all scared on the stretch from Durango to the top of Red Mountain Pass, between Silverton and Ouray. The road is wider there, and it passes through mountains as opposed to hanging from the side of a gorge. The stretch from Red Mountain to Ouray is intimidating to me because of the narrow, winding road and sheer cliffs with no guardrails. It's worse in the southbound direction because I'm closer to the dropoffs. The dropoffs are what makes the drive so spectacular, though.