Jace, Vryn's Prodigy has the text
If there are five or more cards in your graveyard, exile Jace, Vryn's Prodigy, then return him to the battlefield transformed under his owner's control.
What is the point of exiling him and then returning him?
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There are 2 aspects to this question:
Answer: If Jace was simply transformed from creature to planeswalker, he would not get his 5 loyalty counters and would go to the graveyard as a state-based action. A planeswalker only gets the initial loyalty counters when the permanent that represents it enters the battlefield as a planeswalker.
It's also in the card's rulings, indirectly:
In some rare cases, a spell or ability may cause one of these five cards to transform while it’s a creature (front face up) on the battlefield. If this happens, the resulting planeswalker won’t have any loyalty counters on it and will subsequently be put into its owner’s graveyard.
To fully "reset" a creature so that nothing can continue affecting the planeswalker or generally cause confusion, you would have to take care of many things: Remove all counters, unattach auras (there are "enchant permanent" auras that do not fall off automatically) and equipments, end permanent effects that would continue to be active after transformation such as change of controller and color, remove effects such as Cipher, and so on; finally you would have to add 5 loyalty counters manually.
Exiling and returning the creature transformed takes care of all of these issues at once, and, maybe most importantly in this context, it also takes care of any future issues that could crop up from new mechanics and interactions.
Furthermore, solving these issues explicitly would require much more rules text on the card.
In conclusion, the answer is From a rules perspective it's one possible solution that produces a functional planeswalker, and from a design perspective it's the most elegant and future-proof way of doing so.
Nothing would have prevented them from saying:
Remove all counters from ~. Put five loyalty counters on ~ and transform it.
(Note that auras and equipment would drop off due to its new non-creature status.)
But then it wouldn't have "entered the battlefield". For the standard at the time and now, this would have been an insignificant change. For Oath of the Gatewatch, however, there are cards where it specifically and significantly matters (that is to say the primary effect of the card would be negated for these, as opposed to a simple side-effect of the existing complexity of Magic):
Each planeswalker you control enters the battlefield with an additional loyalty counter on it.
At the beginning of each end step, if a planeswalker entered the battlefield under your control this turn, Oath of Chandra deals 2 damage to each opponent.
In order to trigger these new cards, the flip cards would have had to actually entered the battlefield, not simply transformed.