I don't even think the changeover to omnimover can be blamed for the ride's issues, there are truly awesome omnimovers out there after all. It's really down to the execution of the scenes, the dumbing down of the track layout and messy pacing. Lots of problems, none of which I think are the fault of the ride system.
I actually think it entirely possible to convert the Tony Baxter version into an omnimover without even compromising anything of major importance scene-wise. The most interesting and unique thing about the concept's ride system was how it could transition between two levels within the same scene, the transparent layer that separated the scenes allowed you to see into the other scene above or below you. Omnimovers are entirely capable of multi-leveled layouts. World of Motion's track (a somewhat similar variant of omnimover) originally passed over the entrance to the queue at the beginning, guests walked underneath the track. So it stands to reason that you could easily have multiple layers of omnimover track intersecting one another, same as Baxter's concept.
The only alterations needed (which I would consider relatively minor IMO) would be to the track layout used for upper level scenes above the water surface. A suspended track makes it easy to hide the mechanical parts in the ceiling, but omnimovers require a somewhat thick track base underneath the vehicles, something that wouldn't look good if built on top of a transparent faux water surface that you're intended to peer through at the scenes above or below. But even that has a simple solution- just keep the track on the upper level up against the walls so it doesn't actually travel directly over the transparent water surface. One could logically and effectively disguise the mechanics against the wall with rockwork and/or coral reef.
I will however mention in favor of suspended rides- If Peter Pan was longer and had higher capacity vehicles, it could probably eat through crowds much more effectively. Even Baxter's Mermaid concept was over a minute longer than Pan. It also showed two rows of seating. Paris' version of Peter Pan uses higher capacity ride vehicles with an additional row of seats compared to the versions in Florida or California.
EDIT- I'm sorry for getting offtopic here, kind of drifted with the mention of Mermaid...
