1. Have a heat load calculation done on the home prior to purchasing any HVAC equipment. If you have blueprints, doing one is a relatively simple process.
2. Insist on min R 38 insulation in the attic. Don't let them convince you R30 is sufficient, going to R38 isn't that big of a chore and really shouldn't cost you more. Most of the cost is laid in the overhead in getting the truck/men to the jobsite - not the insulation itself.
3. Don't be fooled into icynene foam, it will most likely cause more problems than you'd like.
4. If you can afford a geothermal heat pump system and are planning on staying in the home 10+ yrs - do it. (An entirely different topic).
5. Insist on roof decking with tech-shield. Insist on ridge vents, adequate soffit ventilation. Install an attic tent around your attic ladder if the access is in the home.
6. Insist the HVAC contractor uses mastic around ALL connections (that includes register boxes, plenums, joints in furnace - coil - plenum, duct connections etc.)
7. Visually inspect the HVAC contractors work before agreeing to move forward. Are the duct runs strapped off the floor with minimal bends, kinds, etc.? Is the drain pan large enough so if your coil were to spring a leak (which it most likely will later on) that water will actually go into the pan?
8. If you plan on closing any of your bedroom doors at night, ask that the system be sized/designed with a return grille in each bedroom. (Helps with cooling each room properly - and also reduces stress on the system.)
9. The windows you get will most likely qualify as "energy star". Just make sure they install the windows with the low-e coating pointing the correct way. The last thing you want is for the coating to be pointing into the house... talk about a hot house. (I've seen this done before and the homeowners had already bought new AC systems bc they thought the old ones were too small, etc. etc. etc.)
Are you looking for brand recommendations too?
American Standard & Trane are the EXACT same pieces of equipment... different names & marketing. Similar story for Carrier & Payne,Goodman & Amana, and Ruud/Rheem (Carrier & Payne/Goodman & Amana may have some slight differences, but not much and are essentially the same equipment.)
The only recommendation that I'll make is that the Carrier/Payne variable speed furnace/air handler is pretty fantastic. American Standard doesn't have as many 16 SEER matchups with their VS handlers.
If you live in the great state of Texas, you simply must have a variable speed furnace. There isn't much sense in going to a 90%+ efficient furnace, unless the cost is reasonable.
2 Stage condenser: only if you achieve 16 SEER with the condenser, coil, furnace match up. It is important to verify the con/coil/furn achieve at least 16 through the ARI Certificate. There are some system matchups where the condenser and coil are labeled "13, 14, or even 16 SEER" but don't actually achieve that. The inverse is also the same - some 13 SEER rated condensers achieve 16 SEER with the right coil/furnace matchup.
If they match up, a 2 stage condenser will help immensely. Think of it this way... During the cool(ish), warm, hot, super hot months you have different heat loads on the house. You don't need 100% of the compressing capability every day of the year. Having the capability for the system to "step down" a gear and use less of everything can truly help.
Sorry for the long post, but I believe it makes sense to throw as much info at you as possible when it comes to the HVAC/energy efficiency standpoint as possible to save time/money now.