Went to San Ignacio Mini first and got the tour, although they seem to be adding multi-lingual information systems around the site. This provided a nice overview of the missions and provided background for visits to the other two nearby sites. San Ignacio Mini has been partially reconstructed, ie the walls have been rebuilt and the land cleared. Loreto is just being preserved and so the jungle is being kept under "control" but the ruins aren't being touched aside from some archeology. This makes it a challenging visit, there are signs at the various components of the mission but its still a walk through the jungle. Santa Ana is the "just right" site in between them. The central plaza has been cleared to give you a good idea of the scope of the site and the ficus trees have been removed from some of the walls and reconstruction of them taken place. Interestingly the cemetery here was reused so there are a number of burial plots.
I would recommend that you try to see Santa Ana and not just San Ignacio Miní although it is worthwhile to also visit Loreto too just to see how much work has been done at the other sites.