The Doctor finds that his soulmate marks are never simple; never straightforward. New marks appear with every regeneration, and sometimes even when one of his marks turns colorful, others stay black.
Rose takes his hand and both of their palms look like rainbows.
He regenerates. She catches him and some of his new black marks turn colors. It's okay that not all of them are for her, because she's still got this black streak near her ear that looks like lips.
Madame du Pompadour knew the Doctor was her soulmate all her life, even before she grabbed him in order to kiss him. If only she had made more of an effort to restrain her hands, the colors could have been on his lips, she lamented later in life.
The Doctor can't begrudge Rose a less complicated life with a man that has the courage to tell her things she deserves to hear. He only wishes quietly to himself that his soulmate would stay with him. It's raw, and it's something he's reserving for Rose, even though he knows full well he has other black marks on his body.
He avoids touching Donna for as long as he can, and she does the same, until he catches her to save her life and they both gasp. A quick search has them both heaving a sigh of relief; they're not soulmates.
The Doctor takes to hiding from his companions that he's fallen in love with them. It only leads to heartbreak. Martha never knows. Captain Jack Harkness never knows. When they tell him their black marks are now colorful, he says he's sorry, but it happens when you're always running into people while running away.
The Doctor didn't know Astrid was yet another of his soulmates until after she was gone.
Donna has been saved by the library, and in her virtual reality, she and the stuttering man have the same rainbows on them. She comes out of the simulation and watches as the color fades back to black. It must have been a fluke.
The Doctor met River Song when he and Donna landed on the library. He can see where she's got her rainbows and he says to himself, "Finally, someone I can't fall in love with."
Later on, he finds the places where she left her mark.
By the time the Doctor meets Clara, he's seen some things.
He's seen his two best friends - whose color marks have been on them since childhood - get married and die. He's met the embodiment of his TARDIS and wasn't surprised that they shared a mark. He's given River Song her first colorful marks and gotten married to her. He's found her and lost her over the years, and he notices that sometimes she has more colors than at other times. He still has some black patches himself.
When he and Clara first touch, it's less important than saving the day, than getting out alive. Every time he meets her, she turns another of his black marks colorful.
He never has time to dwell on it. She's tricky, this one; always getting herself into trouble - almost as much as he does.
He mourns with her when her soulmate Mr. Pink becomes a Cyberman - they were more suited to each other than he and Clara.
There's never time to really ask about himself and Clara. He'll joke occasionally, but they never get around to it. He regenerates, and it's the same old routine with Clara. Although he finds that he comes across more brusque, more cross, his new black marks still turn vivid Technicolor when she touches him for the first time.
By the time Clara makes a vague mention of the bond they share, it is once again too late for the Doctor and his soulmate.
It's the same way with River Song, too. On their last date, he wishes that every touch she gives him would be as colorful as the first one.