Crikey, this got really complicated; here's my ten pennies worth.
On my iPhone 5C, because I only had 32GB storage available, I'd only chosen some 62 of my 200+ playlists to sync; this worked quickly and perfectly.
Now I have an iPhone 6 (Plus - not sure it matters a whole heap), with 128GB of storage and which I set up from my 5C's backup. This went fine.
Then, because I now have the space for all 39+GB of my music, I selected "Entire music library" and pressed sync.
This took a long time, and once it had finished, I checked out what had been installed on the iPhone; this was the original 14GB of my selected playlists from the 5C; even though I'd asked for all my playlists. Too, because iTunes, poor thing, seemed to be really confused, possibly about the conflict between some playlists and my later instructions for all, the sync process went on, and on, and on. With no satisfactory result.
I checked in thee forums, and noticed a lot of people suggesting pretty much everything, some solutions which worked and some worked for some people, but not for others. I didn't try any of these solutions; my solution was, somewhat drastically, to deselect all the playlists I'd originally selected for my 5C, and which were stubbornly being applied to my 6, and then just selected one playlist which I knew only had one song in it.
Then I hit sync again, but the coloured bar at the bottom showed I still had 3000+ songs on my iPhone. The sync went on for a long time, with nothing apparently happening; one sad iTunes just kept its wheels spinning, trying to figure out which instruction to follow; in the end it was taking so long, I force quit iTunes, which was not a comfortable idea.
Having left the screen with, apparently, my 3000+ songs on my iPhone, after I reopened iTunes, lo and behold, I only had one playlist on my iPhone.
I then, bearing in mind that I'd force quit the last time I was in iTunes, did a sync, and this went through very quickly.
Progress of sorts.
I then select the "Entire music library" and dived for the sync button again. Once all 7951 songs (39+ GB) were transferred - this took a while - a subsequent sync went through without difficulty, and, more to the point, as quickly as could be expected, in about 10 seconds, which might be what to expect considering nothing had changed.
This worked for me, in that I now have all my playlists on my iPhone, it's just a pity that I had to jump through so many hoops to get there.
I hope this might help others in the same boat at I was.