tried the same thing with me. The system is very nice and definitely gives you less to worry about.
I personally bought a 50g and took pride and picking out all of the equipment on my own. I really felt like it was my tank that I was building and not something that was being handed to me.
Really its up to you either way, I actually built my 50g with protein skimmer, mech filter, lighting, tank, power heads, and everything else needed for less then what the LFS
was asking for the system (I did a lot of shopping around).
The system is very nice, but a larger tank gives you a lot more options and to me was a lot more fun to build.