Personally, I went for an 07 model, which are all "Limited" but without the Limited badging.
I wouldn't pay extra for limited. I'd be looking for the lowest priced bike with the best maintenance with the lowest miles. If miles, cosmetics, and accessories (e.g., exhaust) are equal, look at the condition of tires, chain, and sprockets, which can rapidly increase the real cost of the bike to you.
After 2003 with the starter fix, there is very little to differentiate the bikes other than colors or black vs. silver frame. And before 2003, you can beef up the starter bearing support, so even that would not be a big deciding factor to me.