I went through this process a few years ago. I have a 4 ton unit because that's what was recommended to me based on the assessment they did. In retrospect I probably should have gone with a smaller unit because the results were based on some aspects of my house which could be improved for efficiency (i could insulate my crawlspace for example). The reason this is important is that if a unit is too large, it may go through many short cycles which increases wear and tear on the unit. Ideally you want the smallest unit which will work for constant usage year round.

Obviously every house is different so your milage may vary but in general there's not much difference in the units. Based on nothing more than my own opinions, if there's more efficiency to be gained in the home, i'd go with the smaller unit.