Here are a few of the bigger secret bases in ORAS:
- The one in Route 110 (island like structure next to a sign)
- The one on Route 120 (a small opening in the walls)
- Another one on Route 120 (a tree)
- The one on Route 119 (complicated, see the source for more info as to how to get there)
- The one on Route 118
See here for more info as to how to get to these bases.
If there's any other big bases that I haven't covered in this, feel free to put it in the comments.
Hope I helped!