You mean this guy?
Hmmm... well is just like real life. There are times in which the mc chooses the "right" girl like in Shuffle. This is just related to what the author thinks, like it was said before it depends on what as a man he thinks he deserves or no matter how shitty the girl is he will remain loving her. In real life you see this all the time. The guy prefers the bad girl and the girl prefers the bad guy. The moment I know is like a harem anime I don't even dare watching it
Is that all? Terrible couple choices? Granted, forced romances and "couplings" are about as torturous as the forced romance in Star Wars Episode II. I mean, I just finished watching "So I Can't Play H", its first 8 or 9 episodes were okay, but its ending with Erosuke ending up with Lisara made me want to go on a killing spree. But the shitty male protagonists to me at least is usually limited to Harem animes. My personal problem is many of them like Kohta from "Elfen Lied" are just so unnecessarily awkward it's a little uncomfortable to watch. Sometimes it is understandable, like Shinji from NGE, he's young teen going through puberty and has had a rather troubling childhood. Other than that, there are plenty of male protagonists I find enjoyable such as Tatsumi from Akame ga Kill, Eren from AoT, Kirito from SAO (Yes, I don't care for it either, but he is not as bad as others), do I even need to mention JoJo?
I think it's less about the dumb decisions they make but more about how they never go into WHY they love a certain character or craft a strong a narrative reason why characters would have strong feelings for each other - there needs to be a solid reason as to why because falling in love with someone just doesn't happen IRL the way it does in most anime. One of my favourite romances ever in anime is easily Ryuuji and Taiga from Toradora because of the sheer amount of drama and the huge amount of events that happen around them that constantly bring them closer time after time as they finally realise they love each other and not the people they're trying to hook each other up with and it all happens over a much more realistic frame of time. I love my romance but I don't like when it's shoehorned in there is the most unnatural way possible, requited or not.
I feel your pain OP. Have you checked out the protagonists of Konosuba or Gamers!? They are not all cut and dry. Gamers! throws me for a loop every time the protag opens his mouth!