Well obviously a bad intercooler is going to be worse than nothing at all. If it's basically not able to do any cooling worth talking about and is unduely restrictive to the flow then sure replacing it with one that has good flow and actually does some cooling should result in power improvement. But it's going to depend a lot on the actual car, and I would have thought most modern cars don't have nearly such crap intercoolers in them.
To be honest. The most I would bother doing tuning wise to a standard turbo engine is get it chipped by a reputable company. Assuming it's the kind of engine that responds well to being chipped. Like the VAG engine do.