With many Catholic weddings, it is required that the ceremony be performed in the church itself. With some other types of weddings or officiants, you can choose where to get married. I've photographed weddings in multiple different locations and I'd love to tell you from my perspective the pros and cons of church or indoor wedding ceremonies.
Churches can be extremely dramatic in architecture or interior design. While this might not be for everyone, it can create some amazing images for the modern couple.
The religious and emotional connection with your church can make the ceremony all that more special if performed at that place of worship.
The venue of a church usually provides plenty of seating for your guests, and you don't have to deal with renting chairs.
Which brings me to another point: no rentals. You probably pay the church for the venue, but you won't have to rent the chairs, an altar, or other decorations. So many times, the church is the budget friendly option.
Some churches do not allow flash photography, which can limit the abilities of getting sharp images, especially if the church has a dark interior or not many windows.
Some churches also do not allow any movement during the ceremony. This means as a photographer, I'd only be able to get one angle (plus any second/third shooter angles I bring along). You won't get as much variety.
There's not really any way to personalize the space. Flowers can only go on pews or in bouquets.
While some churches have amazing architecture, there are still just as many that do not provide the prettiest of views.
The best way to make a decision is to discuss the requirements of your church or officiant to determine what's possible. Take into account the look and feel of the site and be prepared for restrictions. Keep your photographer in the loop and get ready for a big special day!