Yeah if forced to choose, I'd go with Flashpoint over Injustice.
Neither is ideal, but in Flashpoint she is at least a bit cooler and not tied to the hip with Superman (he actually fares worse than her in it). Plus it's by a creator who did right by her elsewhere: it feels weird to say that about Johns because he definitely has a spotty record with her and inflicted Jason on us, but he at least started writing her well towards the end of the new 52 and he co-wrote her movies, one of which at least was very well received. That's a low bar but it's still way more than anything related to Injustice has done for her.