Skype supports video calls over internet. Internet goes over 3g.
N900 Skype - tcp/ip - 3g - tcp/ip - Skype

What people mean is video calls that you dial like a normal phone number, without internet.
Phone - 3G - Phone

The difference is, skype is like email, 3g video calling is likw mms.

With skype or gtalk and similar, you need to know someone's skype name. With 3g video calling you use someone's telephone number, like when you send a sms or mms.

People arguing skype and whatever brings 3g video calling are saying approximately the equivalent thing as saying that email fixes a hypothetical missing sms and mms support.
Yes, email "does the same thing" as sms and mms, and we can send email "over 3g", but it's not the same thing obviosuly.