I'd bet that a custom system could beat any off the shelf bits but again cost vs. ease of ordreing and bolting it up. A true high performance shop could easily turn out a one off exhaust to beat anything on the market but at the same time, if you have the time and $$, you probably aren't looking at a $270 Tsudo catback. That said, the guy working his *** off in retail for minimum wage is well served by the budget off the shelf system. Just depends on your goals, budget, and needs.
I think the OTS systems are generally very well done at this point. I don't think you would go wrong. Plus there seems to be an option for everyone in terms of price and features.