The only time I've seen a major problem with using a controller over mouse and keyboard, was in situations where there are many adds, and it's smart to focus on only 1 of them.

For instance, my Static had to change their strategy for A2S, because the member we first had in the Gobwalker was having great difficulty selecting the Bomb at times. We swapped over to me, with my mouse-born ability to click the hate table and the bomb's model, and it went much more smoothly in that regard. I haven' noticed any other noteworthy disadvantages.