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In the episode Journey’s End The Tenth Doctor pours his regeneration energy into his hand and then regenerates into himself. It is later confirmed in ‘The Time of The Doctor’ that this does actually count as a regeneration.

So why doesn’t The Doctor just regenerate back into himself whenever he wants to?

Obviously, in reality it would get boring if we got the same Doctor multiple times in a row, but is there an in-universe explanation? Is it something to do with the Doctor’s Hand that I missed and the Tenth Doctor could only regenerate into himself in this once instance?

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He always accepts - eventually - the need for regeneration.

Even when he doesn't want to "die" and regenerate, in the end, before each regeneration (except of course the one in "Journey's End") he does finally accept that it's necessary for him to regenerate and become someone new. (I'm focusing on New Who here because regeneration was portrayed a bit differently in Old Who, but it's been more consistent within New Who so far.)

  • The Ninth Doctor sacrifices himself to save Rose, knowing that it will mean his own "death" and regeneration. His words suggest that changing his face is the only possibility, but it could be that he hasn't realised yet the possibility of regenerating back into himself, this being before "Journey's End".

    ROSE: Then, why can't we go?
    DOCTOR: Maybe you will, and maybe I will. But not like this.
    ROSE: You're not making sense.
    DOCTOR: I might never make sense again. I might have two heads, or no head. Imagine me with no head. And don't say that's an improvement. But it's a bit dodgy, this process. You never know what you're going to end up with [...] I'm doing it now. Time Lords have this little trick, it's sort of a way of cheating death. Except it means I'm going to change, and I'm not going to see you again. Not like this. Not with this daft old face.

    Another possibility is that he realises that at this point he needs to change. The Ninth Doctor was tough as old boots, still haunted by the memory of the Time War. It was time for him to become the more romantic and happy-go-lucky Tenth Doctor. This is hinted at by the Tenth Doctor in "Journey's End", speaking to the Meta-Crisis Doctor and Rose:

    You were born in battle, full of blood and anger and revenge. Remind you of someone? That's me, when we first met. And you made me better. Now you can do the same for him.

  • The Tenth Doctor's faux semi-regeneration in Journey's End is because, as the Eleventh Doctor put it in "Time of the Doctor", he

    had vanity issues at the time.

    That time, he really really wanted to keep the same face, because he was so gorgeous and fanciable. (Or so I'm told by a number of female Tenth Doctor fans.) This same vanity caused him, only a few episodes later, to become the Time Lord Victorious and claim ownership over the laws of time themselves (in "The Waters of Mars") and to engage in a lot of self-pitying mooning in "The End of Time, Part 1".

    Everything I am dies. Some new man goes sauntering away, and I'm dead.

  • The Tenth Doctor's real regeneration is at the end of "The End of Time, Part 2", after he's recovered his selflessness and will to self-sacrifice. He sacrifices himself for Wilfred, after an abrupt change of heart:

    DOCTOR: Well, exactly. Look at you. Not remotely important. But me? I could do so much more. So much more! But this is what I get. My reward. And it's not fair! Oh. Oh. I've lived too long.
    WILF: No. No, no, please, please don't. No, don't! Please don't! Please!
    DOCTOR: Wilfred, it's my honour. Better be quick. Three, two, one.

    He accepts that it's time for him to die, to change, to become a new person. As he said earlier in the same episode:

    Sometimes I think a Time Lord lives too long.

  • The Eleventh Doctor spends hundreds of years in a lengthy act of self-sacrifice, forgetting his wanderlust and love of travelling the universe to stay and protect the town called Christmas. He turns into a doddery old man before finally being granted the additional regeneration energy he needs to turn into a new person. At that point he's spent so long in one body, and let it grow so old around him, that he doesn't seem to have any trouble accepting the need for change.

    Also, his change may be partly (consciously or subconsciously) motivated by the desire to become someone less "fanciable" for Clara's sake. As he says in "Deep Breath", his first episode as the Twelfth Doctor:

    DOCTOR: I've lived for over two thousand years, and not all of them were good. I've made many mistakes, and it's about time that I did something about that. Clara, I'm not your boyfriend.
    CLARA: I never thought you were.
    DOCTOR: I never said it was your mistake.

  • The Twelfth Doctor goes back to the Tenth-style self-pitying mooning, refusing to regenerate even when the energy is bursting out of his hands, and even implying that he may refuse to regenerate and simply die instead, like the Master in "Last of the Time Lords". It takes him a whole episode of watching the First Doctor struggle with the idea of regeneration - which, if he refused to do it, would cause the Twelfth Doctor to not even exist - to be able to come to terms with his own impending change.

    Oh, there it is. The silly old universe. The more I save it, the more it needs saving. It's a treadmill. Yes, yes, I know. They'll get it all wrong without me. I suppose one more lifetime wouldn't kill anyone. Well, except me. [Doctory advice] Doctor, I let you go.

TL;DR: he doesn't regenerate into himself because that would miss the point. Before each regeneration, he accepts that he needs to die, needs to change, because that's the stage he's reached in his life. Perhaps, too, he always regenerates into the person he needs to be at that time in his life. From the haunted Ninth Doctor to the romantic Tenth Doctor, from the over-proud Tenth Doctor to the slapstick Eleventh Doctor, from the fanciable Eleventh Doctor to the stern Twelfth Doctor, and so on. In "Journey's End", either he had "vanity issues" that he got over later, or it genuinely wasn't the right time for him to change yet. To paraphrase an exchange from "The Doctor's Wife":

Regeneration, you didn't always make me who I wanted to be.
No, but I always made you who you needed to be.

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  • In Journey's End he doesn't use all the regeneration energy on him self, just enough to heal himself, he dumps the excess energy into the spare hand – SpacePhoenix May 8 '20 at 22:37
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In "The Brain of Morbius," the Doctor talks the Sisterhood of Karn. They have an elixir to live forever, and they allow the Time Lords access to it -- but the Time Lords only use it when they have difficulty regenerating. This is because change is necessary.

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