These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ending Fatigue: The World Cup Arc occurs after the team has already won the big game the entire series has been building towards, and is order-of-magnitude shorter and worse-written than what came before. However, the wrap-up, and subsequent Distant Finale at least give everyone their dignity, and serve as an excellent ending to the series.
Ensemble Darkhorse: Rui Habashira of the Zokugaku Chameleons proved surprisingly popular in one of the character polls, where he placed 5th and was the only character not from Deimon or Ojou in the top 10 (well, besides Kakei at the #3 spot). Despite his fairly minor presence in the series, he has a very strong fan following - which is probably why he was revealed to be the mystery player on the World Cup team.
To a lesser extent, Juumonji, who has the most characterization out of all the Ha-Ha Brothers.
To a much greater extent, you have Gokuu of the Shinryuuji Nagas, a character wedged deep in the background who hardly appears at all but has a surprisingly large fan following.
And of course, the most memorable character of the series, Hiruma.
Family-Unfriendly Aesop: According to Kid; Never follow your dreams. Ever. When they play Hakushuu, he turns out to be right.
Though this is also negated by the sheer amount of other characters who do achieve their dreams, so it could alternatively be interpreted as "Never give up on your dreams, even if you sometimes lose".
Fan-Preferred Couple: Though they're only hinted in the series proper, Sena/Suzuna and Hiruma/Mamori do have their own followings.
Foe Yay: Sena and Shin. Their obsession with each other is staggering.
Harsher in Hindsight: After the Seibu and Deimon game, where the rivals are awaiting the Kanto tournament for their rematch? Gets a lot less heartwarming when you know that they wont get a rematch, and all the gunmen have in their future is to get crushed by Gaou.
Older Than They Think: Surprisingly, this isn't the first manga about football - just the first to be successful. The earliest, 5-Yarder, ran from 1977 to 1979.
What an Idiot: Typical reactions to Taki doing anything ever. His idiocy rating is "100%" (which is also a sly dig at his catch phrase).
Monta and Sena sometimes fall into this, too, when proposing seemingly futile offensive tactics. However, sometimes their plans really work...with some Hiruma tinkering, of course.
Wild Mass Guess: Since Eyeshield 21 doesn't have WMG section I will put this here. We all know Monta did chose his jersey number because of Honjo, but Honjo himself did also take this number because of other player, that player being Jerry Rice.