I've always been under the impression that cross-flow microfiltration (CFM) whey isolate is superior. Supposely contains higher concentrations of beneficial substances (beta lactoglobulin, alpha lactalbumin, etc.) than does ion exchange whey isolate.
Ion-exchange whey has a higher ratio of beta lactoglobulin, which is often associated with gastric upset, than filtered whey. Between ion-exchange and filtered whey, I'd go with filtered.