I know it's completely unfair to compare the two shows. I just found myself comparing the two after seeing Fun Home. I'm a gay male, I love Alison Bechdel's work and I love Jeanine Tesori, which is why I was surprised that I wasn't as drawn in to the show as I thought I would be.
N2N had probably the most powerful, emotional impact on me of, perhaps, any musical ever and I've seen a ton of musicals. I found myself weeping several times. As well as laughing hysterically at times. As Ben Brantley said, "A feel everything musical." Despite the fact that they're no gay characters in N2N, it's about a family and we all come from families with usually the other members being straight.
I live in DC and the Keegan Theater just did a fantastic production of N2N and it brought the whole show roaring back to me. I just think the show is breathtaking.
With that said, I know I need to see Fun Home again and watch it on its own terms, not comparing it to another show. It's coming to the National Theatre next year. I'm not sure how the show is going to look and feel being on a proscenium stage. I wish it was going to Arena Stage, as they have a great theater in the round set up there. But what can you do?