There is no problem in forming 3 handseals with a decent speed.
I see certain statements which let assume that he used Izanagi. Itachi obviously knew Obito's power (Kamui), yet prepared Amaterasu to kill him. Obito particularized, that he could survive for the only reason, that he could hide a few secrets from Itachi (and that was not Kamui which he hide from Itachi). We saw no burn marks on Obito's shoulder when he showed himself again.
Once you are hit by the flames, they stick to your body, hence Raikage even had to cut off his arm. At self range, Obito warps away himself, and if his whole body would burn, he would warp himself away together with the flames. He couldn't simply separate the flames from his body (unless you have a scan proving the opposite).
Of course, Kakashi warped away the Amaterasu flames which burned on the trees, but at this point, he created a Kekkai at a specific point to warp a target away (as we know the procedure of Kamui at long range). But at this case, he can't just target his own body to separate the flames which stick to his whole body (also the whole back). You should also consider the pain which occurs with this attack; Obito was thrown off of his feet and screamed of pain. There is no reason Kakashi would be more resistant to it.
Pay more attention to their other techniques, apart of the MS. As Kakashi can use clones, Itachi can use clones (crow clones take even less Chakra). Itachi is fast, makes use of feints and can use crows, which are a perfect counter for techniques which require targeting an object. And Itachi possesses Tsukuyomi, which can only be broken by Uchiha - at this point 2 MS techniques which are hard to counter, while Kakashi has only one.