Well, to start with, the Jensen that’s with Misha is a little more… open? He lets Misha cross boundaries that he doesn’t let Jared cross.
To me, the difference isn’t necessarily because there’s something romantic between J & Misha, but because Misha brings out a side of Jensen that’s a little more self-secure and relaxed.
With Jared, the vibe is very dudebro, and Jensen does a lot of over compensating. He’s got his most masculine, heteronormative foot forward.
With Misha, the vibe is far more relaxed. He’s more willing to do things that might make the audience question his sexuality.
For example, Jensen is willing to dance TOGETHER vs. just on the same stage, more willing to dance suggestively than just like a goofball.
Plus the kind of humor Jensen has with Jared is sometimes (only sometimes!) kinda douchey — generally by making fun of people and insulting their masculinity by calling them “girl” (if they identify as male), etc.
But when he’s with Misha, his humor is full of sexual innuendos (particularly on set, remember 9x06) and he seems okay insulting HIMSELF. He’s willing to laugh at himself around Misha, and I just don’t see that when he’s around Jared.
And finally, when Jensen is with Jared, their joint body language is towards the audience. They’re a team, a brotherhood, facing the audience down.
But with Misha, their body language is towards each other. They’re in their own little world, and Jensen can forget about the audience and just have fun.