It's perfectly fine. You never know when you might get recognized more than you expect! I personally like it when a fellow fan recognizes your character and appreciates you for representing them. You will usually end up befriending and hanging out with these people.
I remember last year at a con I went as Guido Mista from JJBA and two fellow fans ran into me. They were super nice and we had a small talk about how their friend saw a Giorno (from the same series) the previous day, and how the two were bummed for missing that person. Guess what? That person also happened to be me, and I told them about it. They had the biggest smile in their faces and they were so glad that an old-schooler like me is still around doing this hobby XD. We ended up chatting about Araki and JoJo stuff while we shop around the dealers hall before heading our separate ways.
So long story short, it's more than okay to choose a character you feel is less popular. At the end of the day, it really is just about having fun with your character. The whole cosplay experience is enough for me to warrant dressing up silly haha. Recognition is just an extra bonus.