I say go for it. about 75% of what's fun for me is setting things up and watching them develop. Plus there's so many things you learn through running a system. The best part about a reset of a system you know is that you get a chance to fix the things that aren't working while leaving the things that are alone. When you build a totally new system, you can plan as best as possible but it's always the things you didn't really think about or expect to be an issue that you end up hating the most as time goes on.
On my tank, the things I'd like to change the most about the way it's set up can't really be done with water in it (remove internal overflows, completely change the plumbing, etc.), so it's a perfect way to do it.
It will be a cr*p ton of work, but so is setting up a new tank from scratch.
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