The most common complaint I’ve heard is that it’s bloated with too many plugins. You can try the Jetpack Lite plugin to avoid that however.
http://wordpress.org/extend/plugins/jetpack-lite/
As for their business motivation, I can’t give a definitive answer. I’d venture to say it’s related to being a freemium service as they state in their FAQ:
Jetpack itself is, and always will be free. Some individual features
that Jetpack provides will be free, but others in the future may
require payment.
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