The church of the Santa Cruz Mission is actually a replica of the original, built at a much smaller scale. The only original buildings are one old row of housing and a grain storage building. The two museum portions are split, but only a very short distance from each other.
Having been to many California missions, I would say the church does not really stand out. However, I did find the story of the rebuilding to be interesting. What I found the most fascinating was the museum in the old row houses. Not only do they talk about how the Ohlone people lived when the mission was operational, but they talk about the Californians who lived there at the time of independence from Mexico, and then the Irish who lived there during and after the Gold Rush. Different "apartments" were even set up to reflect the different periods in the building's history.
Overall, if you've seen a lot of missions and are pressed for time, this might be one to skip. But if you have even 20 minutes, or if you're introducing young kids to the missions, this is a fun one to see.
This review is the subjective opinion of a TripAdvisor member and not of TripAdvisor LLC.