The disadvantages of CAT6 are price and a little higher difficulty level if you are working with bulk cable. Perhaps if you provide more information as your intended use, we may be able to recommend a proper solution.
CAT6 Cable in and of itself will not improve anything except the maximum amount of cable you can run between computers.
Also, if you're going for gigabit or 10GBaseT speeds, you should use Cat6 for your network. You can use Cat5e for gigabit speeds at short lengths, but I wouldn't go over 50m.
Cat6 cable is designed to better withstand interference from outside sources and within the cable itself (aka - Crosstalk, Signal Reflection). Using Cat6 on a standard 10/100 network will see no noticable improvement over Cat5, and in lengths under 50m, the difference will be equally as small for gigabit.