Stems and seat posts come in lots of different configurations. That means you can choose from several different frame sizes and still get the same good fit.
All other things being equal, a longer top tube will give you a bike with a longer wheelbase, less twitchy handing, better shock absorption, and require a shorter reach stem. Since the down tube, (which connects the bottom bracket with the head tube) will be longer, it can twist a bit more making the frame somewhat less stiff while accelerating, so there is a performance penalty.
A longer seat tube will allow for a higher handlebar position with the same stem and give more room for pumps and water bottles. It can also prevent you from getting as low a handlebar position as you may want. Most importantly though, you should give careful consideration to the longer seat tube raises the top tube and decreases stand-over clearance