The first time he met Zelena in the Enchanted Forest at the Dark Palace Zelena introduces herself as Cora's "other daughter." Rumple replies "That's not possible."
That's a remarkable sentence to say if you take into account that Rumple can see the future. However, it was also said on the show that "the future is a puzzle." Difficult to read because there are missing pieces. He fell in love with Cora so maybe that's why he didn't see it.
In 316 Rumple wrote a letter informing Cora that he knows about Zelena. The letter reads:
Cora, dear. I’ve finally got my hands on your first born. Never thought I’d find her, did you? Now I know why: She’s the most powerful sorceress I’ve ever encountered. Even more powerful than you. Stunning in every way.
Meeting Zelena and seeing her powers Rumple changed his mind training Zelena to cast the Dark Curse because Regina had much more trouble to learn magic. There was never a competion between the sisters. Regina never knew her opponent back then. Only Zelena knew and she was jealous. If Rumple hadn't been under the impression that Zelena wouldn't be able to pay his price (her thing she loves most probably being himself) - which uncharacteristically took him a while to work out - he would've chosen Zelena.
If I didn't know any better I'd say Rumple's admiration for Zelena's abilities clouded his judgement. He underestimated Regina. He only began to praise Regina after Zelena left him. Pedagogical not the best way to do it.