A lot of people, including myself, point out that the Metacrisis Doctor looks slightly different than the Timelord Doctor, and I’ve thought of few reasons why.
In the physical sense, I think its the lack of button down shirt and tie. The T-Shirt makes his neck look longer. In contrast the blue also looks pretty different than the brown when they’re next to each other. If you look at episodes where the Doctor is wearing the blue suit and/or no tie, like in Midnight or Planet of The Ood he again looks different. He also seems to be a tiny bit taller, but that could just be camera angles and unintentional.
But more than that I think it kind of comes down to David Tennant’s brilliant acting skills really. Look at this gifset (X)
Because he’s the same person, playing the same character but you can still see a difference between the two Doctor’s who are the same person. They are clearly both the Doctor and think the same way but still look different somehow.
I think TenToo has more giddiness. An almost innocence to him that Ten hasn’t had since season 2. He seems happier. He smiles bigger, he laughs louder. Which David has also commented on.
I have a theory, and its only a theory. That maybe this is because right before he was “generated” or whatever you wanna call it, the last major thing that he felt was elation that he was by some miracle seeing Rose again. Again, he was born out of his love for Rose.
Just look at the huge smile on his face.
His body language is also a little different, maybe because he’s part human but he’s basically radiating unf the whole time he’s on screen especially in that part where Rose put her hand on his heart.
With TenToo its difficult because, at least to me, its very clear that he is absolutely the Doctor and the differences are so slight that its hard to pin them down but they are there and I don’t think the differences are bad. If anything they make him an even better life partner for Rose.
He’s more human, and that gives him a selfishness that he didn’t let himself have before. He can want and he can take, without worrying about losing it once he has it. He just seems… free.