If I was a centuries-old magic-user, most of the time I'd prefer to remain inconspicuous.

However, if I was a centuries-old magic-user, one of the most powerful individuals alive on the whole of the planet, and could turn into a dragon, I'm sure as **** ain't going to look like just another old hag when flauntin' and swooping around all BAMF-like. Or, you know, when making a display of my awesomely massive stunning magical prowess by essentially "miraculously returning from the dead", even if the witnesses didn't know it at the time.

It's not like it's going to be all Mexican knife fight time between the two looks over which is the one and only canon appearance for Flemeth, or anything. This ain't Thunderdome. I think they work quite well with the situations they were used in.
If she's in DA3, I hope that there is enough opportunities to encounter her as both the crazy old hag and the awesomesauce armor-wearing dragon mage. Heck, I hope we get more than just those two looks for her. She is obviously so much more than she appears to be in any form, after all.