Agreed with this, the first dozen times I flew quad (I was new to kites in general as well) I had one *hell* of a time with tangles. After unwinding I'd spend another hour or two untangling and then be ready to fly ... or more accurately (at the time), crash.
I re-watched JB's video a few times and then one day, it just started working. I wish I could tell you what I started doing differently but I honestly don't think I *WAS* doing anything different. The key seems to be ensuring that when you unwind you're doing the EXACT reverse of what you're doing when winding. The other trick I figured out (I don't recall if it was in JB's video or not) is after I made it down to the kite end, I took a pair of lines in each hand, pulled them tight against the handles/kite stake on the other end and spread my arms far apart. This will move any small mess down to the handle end where it's easier to see. It also will pull out (most) false tangles.
Lastly, if you've got a lot of twists, try and get the ones out where the pairs of lines are wrapped around each other. These are the ones that you would put the handles together and spin them around as a pair to get out. I often start at the kite and and spin the kite around like one of those flag dancers. Sometimes it looks like the lines are threaded together (where you'd take a handle and thread it through the other handle's lines) but they're not, and although it's tempting to do this you'll make a bigger mess for yourself. Wait until you have as much of the first type of twist out before tackling the second, threaded, type of tangle. ... that's a difficult thing to explain, so I hope that made sense.
I've only been flying for about 1.5 years now and I'm usually setup in less then 5 minutes. I don't bother to keep the handles on the line either. I almost gave up after my first few flights, it's super frustrating to have two hours to fly and spend half that time just getting setup. I'm glad I stuck with it though!