When a mysterious organization starts hunting down a self-loathing shapeshifter who doesn’t like using his powers, he and his reluctant girlfriend – the only one that knows his secret – are forced to either take them head-on or die trying.

Your points are taken. I've made another attempt at the logline. I do have a habit of writing too often in the passive voice. Have to get better.

I don't see how writing in the passive voice helps you. Your main characters also act passively ("don't like using powers" and are "reluctant" until "forced").

So, with that said, the protagonist is really the mysterious organization. It's doing things. It's moving the story forward. It's forcing other characters to react. I'm rooting for the organization.

Both the shapeshifter and girlfriend are reluctant cohorts. I don't see her role as adding anything to the story, you might consider defining her part a little stronger or cutting her out.

The dichotomy at the end doesn't work for me either. It's not really a choice because they aren't exclusive. Isn't "die trying" a (possible) conclusion to "taking them head-on?" A choice would be more like, "keep running or fight."

Thanks for your helpful feedback.

They're trying to get him (and his powers) for their own evil use. In general, the answer to your question about her 'reluctance' is both. So I think I'll heed your suggestion and take 'reluctant' out, considering that yes, both forms of reluctance may just be safely assumed. Most anybody would be weary about dating him and obviously, risking their life.

Indeed, my idea for her is that she's a clever character. Not a professor (as it's not quite that age range, think 23-25, and grad school takes a while!), but somebody brainy nevertheless. So she'll be working with him meticulously along the way. I don't want to write her as a weak girl always in need of being rescued, for sure.

Regarding your last question, not sure of the precise details but I have the general idea that violence induced and pain inflicted on their end will (so they hope) be limited. But the antagonists won't return the favor and they'll prefer to use more extreme methods. So they'll have to fight fire with fire. I hope for the shapeshifter, by the end of it, to have more appreciation for his gift and more importantly, for himself and for his (barring a twist, of course) relationship. At the start, he seriously doubts the utility of his power, his capability of even effectively using it, and so on, as he's not even comfortable being himself, but by the end, he should be more confident in all of these facets. Very general, certainly, and I've got to flesh things out.

I like your logline suggestion. I'm going to come back tomorrow with a newly formulated one, taking it into consideration.