First question, what do you plan to keep in each tank? let's say for sake of arguement that you were looking to keep softies in one, and SPS in the other. Well, then you have to worry about the chemical warfare carried out by the softies on one side, killing off the SPS on the other.
A disease in one tank, must be treated in both. While it may seem to be easier on one hand, there are certainly benefits to keeping them seperate. A catastrophic event in one system could very well wipe out the livestock in both tanks. by keeping seperate systems, you allow yourself a potential back-up plan for when things in one system go awry.
Another concern is the equipment. A skimmer that can very effectively handle one system, may not be able to handle two. heating can become an issue as well. multiple heaters off by a single degree can cause big problems. one heater will be forced to do more work than the other. eventually, your heater will burn out from being over worked. Multiple heaters means you will need to get a controller system for them to ensure proper use.