But the poll is kinda weird. I think there's a clear difference between "battle shounen", which are all about superpowers and OVER 9000, and more "adventure"-style series like YnN and FMA. It's strange to compare Emma or Edward with Goku or Naruto, idk.
If going by best moments only, this would be a hard poll, but most shounen protagonists have their quirks and moments where they really get on my nerves. Natsu is the only one I have had zero issues with throughout the entirety of his show.
I was about to vote for Gintoki, but soon i realised that he is more like "adult" shounen (not a seinen). So, in term of proper shounen, it would be yusuke, naruto, ippo, or sawamura for me (the last two aren't on the list).
It's a difficult choice, but i would prefer yusuke than the rest, since he is the type of shounen i would love to see in real life. Challenging every single thing he interest with.
But in general:
Allen from D.Gray-man is one my favorite characters ever for various reasons and so is Yato from Noragami. They are very different from each other, but I love them both and they have a lot of depth too and are highly likeable to me in addition.
Allen appears as typical shounen protagonist at first glance, but he also seems very natural and realistic to me, he is intelligent, although does many things out of low self-esteem and doubts about himself, still he is very resilient and resourcefull. I could write an essay there lol Rarely has seen a character, who touched me so much. xD
Also he has great dynamics with the other main and some side characters.
Yato appears more superficial on the surface than he is. He has some interesting opinions about various stuff and problems letting the past with Nora and Father go to begin a new life. All in all he is a very fun character to watch and interesting.
He also has these great relationships to Hiyori, Yukine and others, which make him likeable to watch.
Oz from Pandora Hearts - very likeable, intelligent, has depth and also a psychology you could get behind. His family history and all is sad and I loved him for that and his character, also his relationships to others like Alice, Gil or Echo etc.
Tanjirou from Kimetsu no Yaiba - I love people, who care a lot and have empathy and I think he is believable, interesting and very likeable. He is fun to watch and I love his dynamics to Nezuko and the others.
Yuu from Owari no Seraph - I know some might disagree here, but I think he's very interesting. He has such a low opinion about himself that he "wants" to be used by others and in general, his mind is not ... healthy (uhm none of them is, but especially him). And I'm quite fond of him.
Also Guren in his novels counts, I guess. He is somehow less likeable in the typical sense of being likeable, but in his novels, he is more likeable than later in the series. He's actually very interesting as person and Shounen protagonist.
Lag from Tegamibachi - Such a sweet kid, you want to protect him haha Very likeable, resilient and so. He is interesting to watch, because he still appears as a kid in some ways, but he manages to go through that.
All three kids from the Promised Neverland - Same. I like all of them. They are intelligent, I love their dymamics and personalities.
At first I wasn't sure about Ray, but still it was quite obvious from the begin and I really like Ray too.
Emma is my favorite of them tho and that has "egoistic" reasons. I was like her a lot in the core (besides the athletic part lol), when I was her age and... well.