Well, the "BGS influence points", normally given to the faction controlling the station where you sell the data at, are wasted if the data is sold to a carrier, as carriers are never affiliated with factions. If you don't care about the BGS (and many explorers probably don't), then this isn't a disadvantage. But for those who do care, selling exploration data is one of the most powerful things you can do to elevate a station-owner's influence levels.
For me, I'm not going to waste all that potential influence by dumping all my data at a carrier. I would/will use a carrier only for the sale of critical systems (eg. some super-amazing discovery I want to brag about on the forums straight away).