1. An additional potential point of failure 2. The core software (a DB, in this case) can (and probably will) evolve independently of the third-party tool--thus introducing an additional layer of maintenance problems.
I'd argue further--and this is of course just an opinion--that such a basic feature as this ought to be supported out-of-the-box by anything that claims to call itself a "database" in the sense that MySQL does.
It's an industry-standard tool and one of the most respected forks of MySQL. It's not a layer of maintenance problems and they sell commercial support.
Their customers include the BBC, Yelp, and Cisco: http://www.percona.com/about-us/customers
Also, for the record, Oracle added online schema changes in 5.6.
This has saved our bacon a number of times. The only kind of DB-related downtime we have is when we're doing a Postgres upgrade.
The MySQL startups tended to say "We love MySQL. We've gotten in the habit of taking an hour or two of downtime in the middle of the night every week to run all of our schema migrations, and we've had to build our process around that, but one we had it in place, everything's been fine."
The PostgreSQL startups said "We love PostgreSQL. We run schema migrations in real-time during the middle of our workday, and we don't have any problems."