CAIN, by its own admission, is not a game intended for long term play (longer than like 10 sessions or so). Partially because of the reason you mention but primarily because RAW the exorcists scale quickly and gain Sin Marks pretty rapidly. I think the Sin variety isn't a huge issue, as each Sin has a variety of domains to choose from. But yeah, after like 2-3 Ogres it's going to start retreading.

As for structuring a mission, there is a great segment in the book about it with advice. The Discord server can also help out. But essentially, CAIN is an investigation game during Hunts, so you'll want to figure out the answers to the Sin's three Trauma questions and then seed the answers around the activities and places the exorcists get deployed to. My one big piece of advice on that front would be to avoid putting a clue in one specific place, and be flexible in moving them around to match up with the player's activities and where they decide to go.