Ready for a monkey wrench? Don't go with a two zone system, go with a six or 7 zone system! Huh? Ok here's what I did and we LOVE how it worked out. I moved into a run down 40 plus year old house with all original everything including the HVAC. On a hot day it ran constantly and never cooled the house below 79, which is way to hot for my wife.
After some research and a tip from my RE agent, I scaled the duct work down to only cover the common areas - LR, DR, FR and kitchen. I removed the ducts from all the bedrooms, baths and hallways. I replaced the ducts that fed the common areas with new, insulated ducts and new registers. I was then able to replace the AC with a 4 ton instead of a 5 ton, and it cools the common areas great.
Then I installed a Mini Split system in each bedroom. You can install single units, or double,triple/quad units depending on your bedroom layouts. The mini splits cost about $700 each, plus installation which can be DIY if you're handy, or about $500-$700 if you hire it out. The mini split units cool and heat, almost silently, very efficiently - 23 SEER is not uncommon, the lowest they offer is 16/17 SEER.
Here's a link to a what we installed in each bedroom.
Now we simply turn off the main central AC at night, and turn on ONLY the mini split in the bedrooms that are occupied. For us with one child, that means two small mini splits running on low, and our electrical usage confirms this is much cheaper for us than running the central AC overnight. Also we never cool any rooms that we're not occupying. We ONLY cool the rooms we're in, common areas during the day, bedrooms at night. We have 5 bedrooms total, and the central AC, so its literally six zones - 1 big common zone and 5 bedroom zones, all fully customizable.
Your situation may be different, but for us this gives us perfectly customized comfort in each room and a lower total cost than running Central AC overnight, cooling the whole house, when we're sleeping in two bedrooms. Frankly my 3 year old son doesn't like it that cool so he only has the cieling fan running, saving even more money.
Just a suggestion if you're redoing everything, large central AC isn't the only option. If you're going central, I can vouch that the Goodman higher end two stage stuff is really nice quality.