I've probably had more the problem that I did dress up as a character from a relatively popular series, but the costume was so simple that unless I was in a group, no one got it.
At this last SCon, that probably applied to both my Watanuki (xxxHolic) and Tres (Trinity Blood) costumes, though probably more Watanuki because it's just the school uniform. With Tres, people probably stopped caring when they realized I wasn't part of the D-Grey Man sets. ^_^; I swear, every time I saw a long black uniform with white trim, I half thought another TB cosplayer, but no. D-Grey Man.
I remember my very first cosplay was Leon from Resident Evil/Biohazard 2. I swear maybe five people knew who I was. Again, this was back in 2000 when RE costumes weren't as common.
Both of my Kumori '06 costumes fell into the obscurity category. My Ouendan uniform got a handful of people recognizing it. But with my Kuroyanagi (Yakitate JaPan! "Yakitate 9 version"), I think I got two people. Well, I'm counting the group who cosplayed Yakitate Japan as one entity.
Most of the other people who say they'd seen YJ haven't seen the last arc which is where my costume came in.
Another obscure one was when I dressed my brother and his friend as male versions of Mature and Vice from King of Fighters. Only one person recognized it. I mean, Mature and Vice are obscure as it is. And to make them male form, that takes hardcore fandom. :3 It's for this same reason that I'm reluctant to follow through with making Prince Peach and Prince Daisy costumes. Really, no one's gonna get it.
Oh... I cosplayed as Shigure from Fruits Basket one year. It's a grey kimono and I wasn't around a group, so that was lost on pretty much everyone. ^ ^;
I cosplayed as Laguna Loire the previous year, and one guy only really knew me as "the guy from FF8 who looks like Sandra Bullock".
Oh, and the male trainer (Yuki/Brendan) from Pokemon Advance. He didn't make it into the cartoon as far as I was told, so no one got it.
Okay, enough out of me. ^ ^;;; *end rant*