I've always enjoyed choosing the individual pieces for my SW setups. Granted, they usually all end up being Marineland, anyway but I like knowing that I've chosen the best possible pieces (lighting, protein skimmer, sump, pumps, etc.) for what I want to do.
Also, if you choose to upgrade, that entire setup is going to be useless -- at least when you build a system piece by piece, you can usually re-use some of the parts in an upgrade, at least to start with, and then replace them as the money becomes available.
Not to mention that you could probably piece together a much larger system for what those nanocubes cost... that means more corals, more fish, more fun!