I think Merida might be a trickier character to include in the lineup, unlike Tiana and Rapunzel.
The only thing that may hinder Merida's inclusion in the line is that she's Pixar while the rest of the princesses are Disney. I don't agree with the reasons you've provided because other more rebellious and feminist characters in the line like Pocahontas and Mulan have been included. In the same way that Disney Consumer Products has homogenized all of the princesses in the line and stripped them off their individual personalities, they will do the same thing with Merida as well if she's ever included.
I expected my reasons to be kind of tricky to explain, but let me explain myself one more time...
I am very well aware that the Disney Princess lineup has characters that don't fit the typical princess archetype and exhibited different behavior like the two girls you mentioned. However, Pocahontas was designed to be very feminine and eventually fell in love. Mulan wanted to be a bride, and thus she tried to be the ideal vision of beauty as presented in her story. And even though she did don an armor and was a warrior princess, she was very feminine and eventually fell in love.
Merida is an almost drastic change in terms of what people have come to expect out of a princess. Like I said, she enjoys being a girl and is quite feminine, but her story is not about her being a girl, much less a girl that falls in love in the most magical way. It is about her coming to grips regarding her relationship with her mother and that she is also a warrior that will go through great lengths to change her fate.
Again, it's very tricky to explain, but Merida is a more established character than the other princesses. The other girls were flexible enough that they could be presented as being stripped of their individuality as you said without anyone really noticing the difference between them and their movie counterparts. Merida is being sold and has gained a fanbase based on the fact that she is somewhat different from the other girls. If she were to be "brain washed" in order to fit the lineup, people WILL notice it and thus create a bigger reaction.
Then there's the issue that you mentioned: she is a Pixar character. I think that's what will indeed cause a bigger problem, not because of legal issues, but because of how Pixar seems to protect their characters perhaps a little bit more than Disney. Sure they love to market the HELL out of them through toys, character meet and greets at the parks and tons of other things. But they do it with the idea that the characters must be themselves no matter what. So Remy is Remy, Woody is Woody, Wall-E is Wall-E, so on and so forth. They are not changed in the most extreme and radical manner in order to meet the standards of a franchise, they are sold on the fact that they are individual characters from unique universes. Merida is part of that group, and part of me thinks that Pixar may not want to let her join the princess lineup since it means that they will be stripping the character of her individuality in order to fit the standards of a franchise.
So yes, Merida has dolls out and such, but she is still Merida, princess of Dunbroch, not Merida, the other red head in the Disney Princess lineup that loves to play tea party and dress up in ball gowns.
Just putting my two cents out.