5. The Height Difference
There is nothing wrong with her height, except that it makes it a bit awkward for the Doctor (physically and emotionally) to adjust to her. The sizable height difference doesn't help the Doctor heal, instead it makes it more apparent that this new companion is nothing like Amy and Rory. There was a moment in The Rings of Akhaten when the Doctor was trying a bit too hard to lean on the Tardis controls awkwardly, obviously, trying to make up for the apparent height difference. He's gotten used to talking to Amy (and Rory) at eye level and putting his arm around her (and Rory's) shoulders comfortably, and Clara's height is a constant painful reminder of what he has recently just lost.
4. She's A Bit Too Flirty
The Doctor is supposedly married, however circumstancially unorthodox the situation, he is still basically married to River Song. Flirtatious advances by Clara towards the Doctor may not be helping endear her to River/Doctor fans (like myself) out there. Of course there is a possibility (what hasn't) that she may be some form of River Song,as many theories around the web would agree with, but thinking of Clara as another person who is a bit too flirtatious with the Doctor isn't helping the character be lovable (snogbox is funny, but really?).