Hours
This is a problem at zoos nationwide / worldwide. Many animals are active at dawn and dusk and are inactive during the middle of the day - the very time zoos are open. Why do they think people want to be at zoos when the animals are resting or sleeping? I say open at lunchtime and stay open until early evening or open just after dawn and close after lunch.
Some zoos here in the southwest are choosing this second option for the summer at least. (Phoenix Zoo 7am-2pm, Arizona Sonora Desert Museum 7am-2 or 3pm, The Living Desert 7:30am-2pm, Reid Park Zoo 8am-3pm).
Also some now have evening hours in summer, daily at San Diego, once a week Reid Park (Fridays) and Desert Museum (Saturdays), once a month at Phoenix.
Extra Admission Fees
This totally stinks. I understand they need the money, but I say just raise the admission to $30 bucks (or whatever) and let everyone go everywhere without the hassle. Two private zoos here in Arizona (Out Of Africa and Wildlife World) charge around that amount and seem to get away with it and I guarantee you they are nowhere near the same league as Bronx Zoo. Plus rural Arizona is not the same as New York City, where people are used to higher prices.
Theme parks like Knotts and Disneyland in their early days used to do this, charge a lower general admission and then make you buy tickets for the rides you want. They did away with that years ago because it is just too much of a hassle and people would rather pay the higher entrance fee and have unlimited rides. I really hate Bronx's pricing setup and if it spread to other zoos it would be one of the worst developments in American zoo history.