C.E. Evans wrote:
If the Yorktown was severely crippled by the "whalesong probe," then she was out of commission for repairs. It's definitely plausible that most of her crew are either recovering from the ordeal, and/or have been reassigned elsewhere during its downtime. Eventually, the Yorktown becomes a quickly-patched up Constitution-class ship just sitting there in Spacedock awaiting a new crew and a new mission. Starfleet decides to rename the ship Enterprise-A and assign it to Kirk's command.
The main problem with this is the time issue. With all that was going on, it doesn't seem to me that Starfleet would've been able to salvage the Yorktown, tow her to spacedock, decommission, rebuild/refurbish, then make the decision to recomission all in the span of a few days. Not if it was that badly damaged. We are talking about government agencies and beaurecrats here, after all.
In addition, the Saratoga didn't appear to have damage that extreme from the probe's effect. So why would the Yorktown?
Also take the corridors and other sets that more closely resemble the Enterprise-D...ie more modern. I doubt the Probe's energies would've damaged the Yorktown to the point where it needed new corridors.
The Ti-Ho theory makes much more sense, as do some others. "Because Gene said so" is not good enough reason to me, considering his history of arbitrarily canon-izing and de-canonizing whenever it suited his fancy or because he didn't "like" something.