I completely see your concern - But I just have to tell you - we love - love - triple love AK.
My kids were 5 and 7 when we went. We spent almost 2 full days there.
I grew up in St. Louis, which has a great zoo. I've been to many great zoos - Washington DC, Cincinnati, etc.
Just don't thind about it like it's a zoo. One can only compare AK to a zoo, if one compares MK to Chuck E Cheese (no offense to my children who love Chuck E, but they are just not in the same realm).
AK is an experience.
If it were me, with a 2 and 4 year old - I would - get there for opening, watch the characters out on the bus. Then, do the safari, and again on FP. The safari feels so different than the typical zoo experience.
Then I would do the Lion King show - which is absolutely exceptional - worth the trip to the AK in and of itself.
Walk over to Kali - if your kids are up for it, ride Kali. My 5 y/o didn't want to ride, but she's always been pretty hesitant. Take in the theming at Kali and in the whole Asia area.
I would skip the bird show, personally - it was good, but it was pretty much what I've seen at good zoos or Sea World.
We were there before EE, so I can't speak to it, except to say that it sounds really cool.
Take a break in the day if you have to after riding whatever rides fit your family.
Then get back to AK in time for the afternoon parade. That parade felt so personal. I guess you aren't technically any closer to the characters than at MK, but it felt like you were. Lots of folks from the Lion King show were in the parade - including the stilt walkers. I loved the parade - a lot. Bought the CD with the Lion King music because of the parade.
Stay hydrated. Prepare to sweat. Rent the double stroller. And enjoy.
Hope you have a great trip!
Leah