Well, the poachers storyline with Wilson and Miss Jobson has changed. Miss Jobson is gone, and it's just Wilson on the radio. Though Jobson still appears in one of the two videos along the queue, and the poaching video with Wilson is still at the end of the queue.
Rather than poachers, the bad guys are now more "elephant-nappers". Big Red is no longer mentioned, and it's just that Little Red hasn't been seen and is then "missing" as you go along. It's toward the end of the ride that it's found out that she's been taken, so you're asked to help save her.
In the new storyline, I don't think Wilson is in a plane anymore, thus the reason the plane was removed from the final scene of the attraction. Before, Wilson and Miss Jobson were supposedly in a plane flying over the Preserve.
I think part of the problem is that people using FastPass missed the Jobson video entirely, and had no idea who she was supposed to be. At least both FastPass and Standby saw the poaching video with Wilson, so he's not a complete stranger when you talk to him over the radio.
-Rob