There are changes that could be made to smooth over some wrinkles, but I don't think most of the changes you brought up need to be made.

if we're going to have the Au Ra in game, how will that be explained considering Yugiri's unwillingness to reveal her identity when she was introduced.
If I remember correctly, she never said it was her race that caused her to hide her face (after all, her race is clearly evident by her tail), but her excuse was something like 'it might cause people undue distress'. She may have meant her race, she may have thought that she personally might be recognized, or maybe she was lying. Life is messy. Even if she did mean her race, all MMORPGs have oddities when it comes to their timelines. An Au'ra player participating in storyline that predates Au'ra coming to Eorzea is just a part of that.

can we fix thancred's dual jobs, is he a rog or pld
Does he need to be one or the other? In game and in real life people can have many different skill sets.

will we see some thing tidied and cleaned to make 2.0 a bit more streamlined, restructure some of the gears, and dungeons and the way the storyline has paced up until now
Are there any specific things you had in mind regarding the restructure of 2.0 gear and dungeons?