William and Sofia is precious! Plus, there are several nn's if it ever feels to heavy for any stage of his life. Willy/Billy for a baby, William for a toddler, Liam for a child, Will for a teen/adult, and Bill for a distinguished older gentleman!
GO WITH IT.
Yes, it's popular. But for good reason! William is a core classic. You can't go wrong with it. Of course a name like that will be popular. I really don't think popularity matters. If you love the name, use it! Besides, I see way more boys named Liam than Will. William has great namesakes, too: 4 US Presidents, Shakespeare, AND Bill Gates!
I love William. It's classic enough that it's not going to date, and there is a reason it's so popular; it's a great name!
I say go for it! William and Sofia are a perfect match.