So I was raised in a Protestant church (Lutheran), and I still attend weekly services and am very involved in my church. I love my denomination, my church, my community, and everything it's done for me. My FI is an Irish Catholic who very much holds his religion as part of his whole identity (went to Catholic school, family is pretty religious). He hasn't been to church regularly since he was a kid, but the Church is very important to him.
My church is very much a go-with-the-flow kind of church, and no one would bat an eye at a Catholic wedding (as, whatever, as long as we're married and Christian and inviting everyone), so I've never really considered the implications of marrying someone of a different denomination. However, now, as I'm doing the research about Catholic weddings, dispensations, locations, etc., I'm not sure I'm wholly comfortable marrying inside a Catholic church (as a location, not necessarily a religion). As I said, we don't have a Catholic "church home", and he's not comfortable with my church, so I was planning on forgoing a church altogether.
Now I realize this isn't really an option in the Catholic religion, and to an extent, I get that. But for us, and for our inter-denominational marriage, I feel like not being in a church is more neutral, and we can find ways to incorporate both faiths in a way that reflects us, as a couple, better. However, obviously, FI is worried about not being right in the eyes of the Church.