One way to ignore a subdirectory is to use "-x <subdirectory name>"
In the following case, you could use "-x a". Note that would also ignore files named "a" but not files "a.txt"
├── new
│ ├── a
│ ├── a.txt
│ ├── b
│ └── c
└── old
├── a
│ ├── 1
│ ├── 2
│ └── 3
├── a.txt
├── b
└── c
In case you want to ignore "aa/bb" (i.e. not comparing "old/aa/bb" and "new/aa/bb"), you need to use "-x bb" so if you wanted to still compare "new/cc/bb" and "old/cc/bb" you would be out of luck.