My blog is a sub-domain, and I have 2 google analytics accounts for my root domain and for my sub-domain. I find it really useful and haven't had any cons at all. The only con I do have though I use my sub-domain for my Salesforce blog and my room domain for my personal blog. When I try to set ad-sense up for the sub-domain, google looks at the content on the root domain, not the sub. So I can't qualify for ad-sense on my Salesforce sub-domain because my root domain doesn't have any content that advertisers would want to advertise on - thus restricting me from being able to advertise on my sub domain.

But with GA, it's been solid and I haven't had a problem yet! I hope that answered you're question Rakesh.