I have one...and I don't see much disadvantages. Only gripe I have is the proprietary seatpost...but which aero frame has a round post?
The crosswinds have to be blowing real strong to affect the handling. Its not like you're going to blow off the road at the slightest breeze as some may allude to. I've ridden 50mm, 60mm, 66mm, 88mm. Only time I thought it was really too much was with the 88mm Novatecs.
As for ride quality...the "harsher" ride does not bother me. I run 25c tubulars on my 404's. With the new Cervelo S2/S3...they have the near ride quality of the R series.
Most of Garmin has been using the S3 in the majority of the northern classics so far. Even on the cobbles
http://www.slipstreamsports.com/2014...2014-classics/
Guys that are replying that don't own an aero bike can do nothing more than speculate.