so why did the great and all powerful Rumpelstilskin, the one who created the power within Emma fail to even apprehend him? let alone kill him without getting killed himself?
Well first. Rumple isn’t all powerful. He is incredibly power as the Dark One, but Rumple doesn’t have magic himself. That’s the big difference. Regina and Cora had some sort of spark that let the talent be nurtured within them. But Rumple never had any sort of magic. Emma simply IS magical. It’s the very foundation of her being. She is pure true love magic. And that’s the most powerful magic of all.
Rumple didn’t create the power within Emma. He just made sure that her parent got together to create her. And then he added a drop of their true love to the Curse scroll to ensure that Emma was the Savior of the Curse But–even if Rumple hadn’t been pulling the strings–and somehow Snowing got together, Emma would STILL be the most powerful creature in all the realms. She’d still be the daughter of True Love, Rumple or no.
And Rumple didn’t apprehend Pan because he underestimated him. He never expected that Pan would trick him with a second Pandora’s Box (or real one..I guess). He was all set to put Pan in that box but then was tricked. He later put what he thought was Pan in the box, though in 309. Peter Pan was all about mind games, not raw magical power. Just because Rumple got tricked doesn’t mean PP was more magically powerful, just that Rumple didn’t think through everything.