My understanding is that it is the Friends of the Desert Mountains who have been doing the work of restoring the trail, and I thank them from the bottom of my heart. NeverWas, I like your story of how the Desert Museum got built, but I think it's an urban legend, i.e. a story created imaginatively and collectively to explain something odd. Back in 2004 I interviewed the guy who actually built the Desert Museum trail (for an article I was going to write, and never got around to. ) The guy's last name was Vieth. He was one of two brothers. They were hired by the Desert Riders to build the trail. Virtually all the trails in this valley have been built by the DR, for the purpose of expanding their horseback riding options. (but, it's possible, in support of the "Natural Museum" theory, that the Desert Riders chose this spot to create a trail, because there already was a short existing trail that the Museum naturalists had started. If so, it seems very, very unlikely that it went up more than a hundred feet or so.) Vieth said he and his brother rode up and down on motorcycles while they were building the trail. Judging from what he told me, it sounded like there was a lot of beer involved.

He was something of a character.
The 'loop' that goes up and then down fifty feet is annoying and seems senseless, but when you think about the topography there, it makes more sense. The big "shortcut" climbs very steeply straight up a face, whereas the real trail switchbacks slightly more gradually up the side of the ridge. It then has to go downhill a bit to get to a more switchbacky area--again, more to the side of the ridge rather than straight up. The general principle of hillside trail building is to create switchbacks, not to go straight up, because A) it prevents the trail from washing out and creating erosion and B) because people get tired going straight up, and fall going straight down. Switchbacks may seem annoying, but they are as crucial to the engineering of trails as foundations are to houses. You cannot have a lasting hillside trail without switchbacks. Sorry about that.
I'm begging Skyliners to respect the volunteer's hard physical labor and KEEP TO THE REAL TRAIL. Yes, I'm shouting, because I'm really fed up and angry at the brutal damage done to Skyline by silly egotists who seriously think anyone gives a flying duck in a rolling donut hole about their precious PRs and BKTs or whatever the cluck they're calling it now. NO ONE CARES. No, no one cares in the slightest whether you cut five minutes off your Skyline time by brutally damaging a bunch of plants struggling to grow in dry and eroded soil. Get over yourself shortcutters! I'm slow and I'm proud! There, I said it! If I can come out of the slowness closet, so can you! So stop the stupid shortcutting already!
The real heroes of this trail are not illogical nitwits who seriously think that cutting the trail somehow makes them studly, but people like the Friends of the Desert volunteers who spent sweaty hours painstakingly repairing all the damage the Ultra-Narcissists have wrought.
Ok, rant over. I feel much better now.

Q: How many therapists does it take to screw in a light bulb? A: Only one, but the light bulb has to want to change ...