Pirates and Haunted Mansion are E tickets and Navi is a C ticket. It doesn't make sense to compare them and say it's not as good because it was never intended to have the scale of those attractions; it isn't supposed to be as good. It's a little like complaining that Winnie the Pooh isn't as good as the Tower of Terror.
I don't disagree with any of your suggestions, but again, they're essentially just complaints that it isn't a D or E ticket.
I would love to have a D or E ticket version of Navi, but it isn't supposed to be that. As a C ticket, it's pretty great and probably the best C ticket at Disney World. I wish Disney designed more rides like it, regardless of the scale -- Tiana, e.g., would be a much better ride if it had the detail that NRJ has.
Of course the wait times are too long, but that's just a function of Animal Kingdom not having enough attractions (and also that it's popular and people like it, because people don't wait that long for rides they don't really like regardless of the park).