I do tech support for an HVAC Manufacturer (Haier). Sizing the unit has nothing to do with SEER. It's strictly a capacity issue. Personally, I'd go for the highest SEER you can afford, using R410A refrigerant. Utility costs will only go up in the future.
Years ago, we installed 13 SEER equipment in our home because the builder wanted to put in 10 SEER at an inflated price, so I wouldn't get it from him. We keep our house cooler, and pay less in electricity, than our neighbors in the development who bought the builder's system.
Depending on your needs, one of the new multi-zone mini-split units may work for you. Some use variable-speed compressors and fan motors for greater economy. Mitsubishi and others make them. You get one condensing unit outdoors, which is piped to evaporator units located in different parts of the house. You don't need to run ductwork, which is a big cost savings. These systems are very popular in Asia and Europe.
I agree that the 95% furnace is a better deal. I'd also make sure to get the equipment from a reputable source to prevent warranty hassles in the future. Many manufacturers (Goodman, for one)will not warranty products sold online because there are places selling 'seconds' and other damaged goods and passing them off as first quality.