Well, I’m not an expert but I love the churches of Rome and I can tell there are thousands of churches in Rome. I’ve got the privilege to see hundreds of them (during weddings), and based on my experience, they’re mostly in Baroque style or in Roman style (few or them are gothic too and S. Maria sopra Minerva is a rare gothic/baroque example but I’m not considering the synagogue and the mosque, of course).
In my humble opinion the most beautiful one, in baroque style, it’s the one named by locals as “the chandelier's church” which is SS. Giovanni e Paolo, not far from the Colosseum. Still, in baroque style, you may consider also the church of S. Maria in Trastevere or S. Andrea al Quirinale.
If you’d like the Roman style instead, quite simple and intimate, you may consider the “S. Costanza Mausoleum” or the “S. Liberato” church which is really awesome, but 1h by car from Rome.
There’s also a very modern and contemporary church, but I wouldn’t recommend it honestly as it’s located in a district which I’d consider as not so safe, it's named Dives in Misericordia if you’d like to give it a glance.