Often, the warranty varies only in the cost. Sometimes, they'll throw in a better drain valve on the longer ones (the plastic ones should just be thrown away). In fact, sometimes it's cheaper to buy the 6-year one and buy the store's extra warranty than the factory one with the larger warranty. Think of the warranty as insurance, in most cases, it does not reflect differences in quality. It might buy you a longer or extra anode rod, but you can replace yours far cheaper than the warranty upcharge. Just remember to do it!
A shorter, squatter one may be harder to get through the door. The exterior surface area is the difference in which one is more efficient - smaller exterior area, less radiation, more efficiency. Most of the heat loss tends to be on the top since heat rises, and a larger area there is likely to mean more loss, less efficient. Most modern WH have decent insulation, but adding more should still help some.
The thing that may affect the overall life is if you drain it in the winter - that will add a lot of free oxygen into the tank. Course, running it all winter with no use would cost a bunch, too. Typical potable water already has a fair amount of oxygen, so the difference may not be much.