Imagine they actually put Manafort or Flynn on trial. I mean his attorney is going to have a target rich environment for depositions etc. Various pieces of information during testimony. We would have many things that we have thought... confirmed before it was done. And in the end Trump would give him a pardon.
1. The Mueller team had all kinds of evidence against him that had been gathered through the FISA surveillance last year.
2. The FISA warrant is for intelligence gathering and probably cannot be used for criminal prosecution because of the shadowy nature of the process to secure the warrant for surveillance. Any evidence gathered this way would likely be considered inadmissible in court.
3. Therefore, the Mueller team needed to find other evidence through "legitimate" means that reinforced what was obtained through the FISA surveillance but would actually be admissible in court.