Re: Apothecary gives duplicate recipes after syncing with golden nug.

You shouldn't get ANY duplicate schematics- they work differently to recipes, and after several playthroughs with the nug, I have yet to encounter a duplicated schematic. This time I even waited until Skyhold before using the nug, just to check (well, that and I was doing as little as possible, going for the 'get to skyhold at level 5' trial achievement thing. Got it, yay). I think recipes duplicate because they're treated like requisitions (which you can get over and over again). Changing that would probably be a giant pain, and since patch 10 was supposed to (but hopefully won't be since Trespasser broke so many things) be the last patch ever, I doubt they intend to do anything about it. 😉 
As for having all the best stuff early on... When you've played the game 10 times or so, you might care less about such things. 😛 For me, it's doing different story stuff, etc. Plus, now I have shiny weird stuff from Trespasser to play with, like musical staffs!