The main drawbacks to PushServer seems to be that it's not cross platform, and it doesn't interact with Apple's feedback service. Apple has an ominous warning for people who decide to do this: "APNs monitors providers for their diligence in checking the feedback service and refraining from sending push notifications to nonexistent applications on devices." [1] Though it's unclear what the penalty really is, and this is listed as a TODO item by PushServer [2]
My company decided to build a push notification system in house. We needed it to be cross platform, able to handle very large volumes, and fully follow all of Apple and Google's guidelines. We recently released it as a service for other game developers: https://gamethrive.com
Having built something like this myself and wrestling through the all the edge cases, I've come to the conclusion that unless you have a good reason for doing so, you should outsource sending of push notifications to a 3rd party service. Parse, Urbanairship, and GameThrive (our service) do a good job and are way less expensive than maintaining it yourself, especially if you plan to deliver a high volume or have multiple platforms to deal with.
[1] https://developer.apple.com/library/ios/documentation/Networ...
[2] https://github.com/jazzychad/PushServer/blob/master/TODO.md