Looking back, I can think of a lot of unpopular or controversial anime series I'd say are worth sharing. One series that I'd definitely place under "controversial," for example, would be School Days. Honestly looking back at it, I kind of remember appreciating it since it was the only harem anime adaptation with a harem that had severe consequences, hence the "Nice Boat" controversy with regards to the last episode's airing around the same time there was a murder of a Japanese high schooler IIRC.
In terms of unpopular and recent, I'm not afraid to admit I actually liked how ridiculous Oniichan no Koto Nanka Zenzen Suki Janain Dakara ne!! (I Don't Like You At All, Big Brother!!) was despite its premise (which essentially hinted on a little sister lusting over her big brother). I think what made it unpopular was that people presumed it'd be explicit and get into some graphic interactions when in reality the series actually never went that far and stuck with comedy to the likes of B Gata H Kei (Yamada's First Time - that anime about a girl who wanted to have 100 sex partners but was struggling throughout the series on this one, normal-ish guy).
I guess a lot of the unpopular anime series I ended up liking were all kind of lowbrow romantic comedies, which I would admit is a guilty pleasure for me.
Anyone have their own?