Zelena has the courage (Charming) a brain (Rumple) and it’s speculated that that the heart could maybe come from Neal. I was listening to another podcast just before and they speculated that maybe Zelena would want Emma’s heart, because it’s so powerful.
That led me to think of how Hook went after Belle because that’s where Rumple kept his heart. If Zelena’s been getting info from Rumple, and so knows that Emma loves Neal, (because Rumple ships it like WHOA), then maybe Zelena would go after Neal’s heart as a means of gaining control over Emma’s heart? Emma’s heart can’t be taken, so if someone wants to get at it, they’ve gotta take the scenic route.
Zelena probably doesn’t grasp the parent/child true love thing given her upbringing and her chip on her shoulder over having been given up, so she wouldn’t think of going through Henry to get to Emmma. But assuming Zelena has a lost love somewhere in her past, (let’s face it, she’s totally gonna), Emma’s romantic love would be the course of action Zelena would think of taking, to get to her heart, and that makes Neal her target.