Some drawbacks:
- size of snap/flatpack package
- probably it’s harder to verify whether or not it contains some rouge software
More on size discussion:
https://www.reddit.com/r/linux/comments/4o4u2h/snap_package_size/
Having said that I think it’s a great way for Linux to move forward. For me it’s like one package manager to rule all distros hopefully making it easier and giving more incentive for developers to actually release their software for Linux.