The biggest drawbacks will be a lack of some features being supported and a lack of support for the configuration; you come asking why XYZ doesn't work and the moment you say you're using SAMBA for your domain and you'll have people sort of shrug it off and say that's the problem, whether it is or not.
You also run the risk of Microsoft's next service pack breaking something in the configuration.
You don't know when there are network issues if it's because of a bug in SAMBA or if it's a legitimate problem with your configuration.
In the long run, you're better off using actual Windows Server or the small business server edition (depending on licensing needs) for directory services and keeping Ubuntu as your file server, in my opinion. Nonstandard configurations can work and can work well, but only if you're willing to put in a lot of extra administration time to learning the ins and outs, staying on top of bug reports, and putting up with the extra maintenance it takes to run that nonstandard configuration.
In the sense of keeping an organization running with minimal headaches and being able to focus on other system issues then nine times out of ten I would go with the mainstream approach.