Any character at the end of their advancement would likely have had their advantages and disadvantages for a long time and they can be majorly character shaping. With Disadvantages being randomly assigned, this pretty much mandates that with them changing on a respec that there are going to be major changes to those aspects of one's character whether desired or more importantly NOT. In many cases one's Disadvantages could be RPed as major character traits and this kind of messes up any history of such RP and the whole idea of them changing kind of flies in the face of Respecs not being intended to totally rewrite characters.
In the cases of disadvantages a player cannot accept, there are already mulligen rules for getting a change made to them and having them changed again in a Respec just seems like a forced change that there is already a system for dealing with if it were desired.
