If you need a better PDF reader than iBooks, there are literally dozens of them.
I'm pretty happy with PDF Expert. There is no way to change how bookmarks sort, but they are in page order already.
One software developer, even Apple, can't anticipate and provide every feature every user wants; and if they tried their apps would be so cluttered as to be unusable. That's why there are third party apps, so people can pick the one the suits them best.
I'm sure you can find one that does what you want.