I think popularity depends on where you live too - my nephew is the only Harry in his nursery class at school, and in fact there's only one other Harry in the entire school (a couple of years older than him), so it hasn't been a massively popular name in that area.
For me, how much I like a name trumps its popularity - I have loved the name Noah for years and years, it's super popular now and I still love it!
I guess it depends on how much it bothers you if your child has their surname initial tacked on their name at school - Rockhopper A, for example. For me, it wouldn't bother me if that happened to my child, because although their name might be what they're known by at school, their personality will set them apart from the other Rockhopper(s).
We do have a never formally stated family policy of not using other names though, from family we see often anyway. So already a long list of boys names I can never use (lots of nephews!) 