Just because they've routed calls over the internet up until now doesn't mean this is the only way to do it. There are probably quite a few reasons for not using the data connection. A couple that come to mind are possible call quality issues and wanting to stay on the good side of carriers. We can gripe all we want about how much the carriers and their policies suck, but can you really blame someone for trying to avoid having to battle one of them?
This still covers users who primarily use Skype for international calls and maintains a high level of quality. The data connections on mobile phones can be spotty at times and this way you have a reliable connection to a relay point which in turn uses a more reliable internet connection. I used a VOIP service a while back that worked like this and it was great.
For all we know, they tried VOIP calls directly from the handset only to find out it's unreliable. I use StreamFurious on my handset and I'm disconnected every few minutes so this isn't so far fetched. Or maybe their market research revealed that most users are interested in international calls in which case it's an easy decision to go in this direction to avoid trouble with carriers. We really don't know. It's possible there's a good reason for it.
In any case, they're not being deceptive about it, and for the most part, the result is pretty much the same despite the varying methods. The only ones who are really left out here are the people who want to buy a handset with a data connection and make most or all of their calls for free over the internet. The reality is that they probably make up a small portion of Skype users. Sure, it would be nice, but when the companies building and controlling the networks are still in the business of selling phone calls this is a pipe dream. Maybe one day they'll just provide access to the network but we're not there yet.
I'm not aware of any terms of service that prohibit using the data connection for VOIP calls so someone is always free to create an application that does this. The best part about Android and the G1 is that you can install whatever you want on there whether you have permission from a carrier or not.
