There may have been a deliberate reason for the regeneration being more jarring - or this could be me finding a reason for it - but...
The two previous morphings we've seen have been accepted by the dying Timelord; the Ninth as long as he got to say what he wanted to say, went quite happily, while the Jacobi Master actually welcomed a new body to be a match to the young Doctor.
This time around, the Tenth Doctor stepped into the booth believing he was going to die - it was an out-and-out time to end it all decision. Then it didn't happen, he slowly began to regenerate, which for him, I think was worse - he might have been prepared to end it all, but not give up his life for the next body. And that comes across clearly in the line, "I don't want to go".
Then watch him - the regeneration process is much slower than before; it's not sudden or bright or violent. It;s like he's initially dissolving away before it kicks in.
Now remember when the Master refused to regenerate and chose to die?
I think the reason for the awkward change is because right until the end, the Tenth Doctor is fighting the process. Unlike the Master, he won't stop it, because he's accepted his fate is to move on rather than die out-right, but he's clinging to every second he can, and resisting the Eleventh Doctor's birth.
So the new Doctor has to fight his way through the dying body, rather than have the normal process of the last incarnation give up to cheat death.