John Jones has two businesses, each with their own EIN. He deposits $11,000 in the morning for business A and $15,000 in the afternoon for business B.

Are the deposits aggregated on the CTR? - two Section As and one Section B, multiple persons and multiple transactions checked with two account numbers?

It would seem that separate CTRs would be cleaner, but is aggregating required because of the commonality of transactor? If each transaction had been done by different individuals, the CTRs would be separate (unless of course if there's co-mingling)

Personally, I would aggregate. One conductor (Section B); two benes (Section A) since I had notice that the conductor was the same.
I would think that either way is appropriate and would meet the spirit of the law.

First, determine what types of business organizations you're dealing with. If both are sole proprietorships owned by Jones, you don't have an issue. You aggregate based on common account ownership, even though the businesses have EINs. In this case, you'd file with John Jones in Section A, with at least one of the DBA names in item 5, and "conducted on own behalf" in Section B.

If the businesses are separate entities, then you must aggregate based on the conductor (Jones) and file a single CTR with two Section A entries and one Section B entry.

You're right that if the businesses are separate entities and different individuals conduct the transactions, you'd have two separate CTRs.