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I would choose the company that can explain to you how they're going to set up the system to take the most advantage of the multiple-speed/variable speed fan motors. The half a SEER is great on paper but if the system isn't set up correctly to take advantage of it you're likely not going to ever see the SEER difference. I would want to hear about how they've used, at the least, ductulator and how they'll come in and balance airflow according to requirements for the heat load/loss of the house. I would make sure you get a service warranty along with an equipment warranty because it's likely $100/hr or more for service whether the part is covered under warranty or not. At the very minimum 1 year should be given to you for free service if anything is wrong with the system. I would want to hear how they're going to check all the duct work and seal up any sections that need to be if needed. I would want to know they're going to provide all paperwork and how they'll pull all permits.
When you do make a decision, when the team shows up to install, have breakfast for them and throughout the day provide them with drinks and ask them if they need anything while they're there. I know this sounds like overkill since you're already paying to have it installed but you want them to be as comfortable as possible because humans tend to make bad decisions when they're frustrated and uncomfortable. This could be true for your doctor or anyone else providing you with a service.
You're about to sign a long-term contract with a company so I would want to make sure they're going to be there for you when you need them and that you feel completely comfortable with the company that you choose.
And for God's sake, or Allah's (or whoever), get a PM contract and make sure you know what's spelled out in that contract. Believe it or not most major failures are preventable and the damages can be mitigated if caught early.
Ask them about your return vents too. Too many times I see return vents that are too small and you have no wiggle room for what type of filters you have to use. It's el cheapos and if you use anything else it'll be detrimental to the performance of your system. It's better to have returns that are too big than too small. Too big will allow for higher filtration filters and a more effective capture rate for particulate. Once you go above 500 feet per second on the return side of the HVAC system your out of range for even the crappiest of filters.