Not hard to relate to a character who is a genuin loser or jerk... it is just that you can't get them to do exciting things.
However let me scale this down since we arn't going to find ANY genuin loser in anime who is also a main character.
How about overt character flaws that are genuin character flaws? (No I am not counting... for example... Luffy's Inability to swim)
One anime actually impressed me because the character's main flaw (in that she was inexperienced) actually stuck (until... the continuation... but lets ignore that) until the very end. While her main trait (Super taste) was actually played out less.
It wasn't something that was compensated, thrown into the background, or only convenient when the plot calls for it or more commonly "A possitive trait only treated as negative". It was an everconstant flaw that the character had to work around with great trouble. This was unusual.
The Mightiest Diciple actually outright annoyed me with the constant mention of how much of a loser the main character was... Inspite of the fact that through sheer will, determination, and Obvious Talent (that is ignored by the anime) he ends up the best anyway (even now I believe they HAD to have just said that so he wouldn't get pig headed). Heck the male lead of Oh My Goddess would also be in the same league where he was unliked and considered unattractive inspite of his great personality, good looks, and the fact that he genuinly doesn't seem to short most of the time.
seeing dozens of generic main protagonists you kindof end up craving something different even if it means the main character is a murderer.
I sort of wanted to see a character who wasn't either
A) A perfect character with flaws ("I have perfect emotional intelligence. What was that? I ignored my own feelings? Well because I am perfect I instantly cast off this flaw")
or
B) A perfect character who we are told has flaws. ("I have no talent for running, inspite of the fact that I run faster then all the other characters")
or
C) A perfect character who is just unlucky except when they are not ("Dang, because I was caught in the bathroom with those girls they think I am a pervert... good thing this won't prevent me from making them ALL fall for me")
Which are essentially the three types of anime "losers".
Edit Addition: I forgot D) A Perfect character who is disliked as their flaw ("I hate you for no reason!")