Yeah. Usually, I'd want to turn super to get rid of an act boss, but otherwise, double jumping wasn't a problem for me in S3&K, as I never used it much unless I had a shield. Knuckles and Tails, however....
....But anyway, as for SRB2, there's no way I'd want thoking to be overriden by transforming into super, though. If I do accidentally transform, though, I try to make full use of it.