What to look for in a new furnace
From a payback standpoint, its might be hard to justify much above 90%.

One feature I really liked was a variable speed fan direct drive and two stage burner.

Having the variable speed blower means you can leave the fan on and it will circulate at low speed. This helps equalize temp and humidity, plus there is less dust, as the filter cleans continuously.  

The two stage burner means most times, the gas fires slowly and the system recovers the most heat.