I find that flaked wheat has a lighter, crisper graininess while flaked barley has a much more pronounced graininess that I find clashes with pale beer. One of the saving graces for flaked barley is that the amount of beta-glucans in it is about 10 times that of flaked wheat, so you could use quite a bit less flaked barley than flaked wheat and gain the head and mouthfeel while possibly avoiding the flavor impacts. However through a bunch of brewing trials, I found that I could always taste the flaked barley in a negative way...even when I reduced its percentage to less than 1 percent. Those beers still had huge heads, but the flavor impact was too much for me. I've since moved to flaked wheat exclusively when I want a bit of head and body insurance and I find the crisp wheat graininess more refreshing and unobtrusive. By the way, Tasty McDole has found the same thing and he often includes a minor percentage of flaked wheat in his recipes.
One beer that does tolerate flaked barley well, is dry stout. I think that the roastiness melds nicely with the fuller, flaked barley flavor and does not diminish the beer.