Even a complex system can be fine if it's represented accurately and consistently. In fact if done masterfully it can really be something amazing. Kishi's chakra system is so far away from accurate and consistent that it's hard to even talk nicely about it. If my watch/read through of Naruto were put into a conversation about the chakra system, it would look something like this:
Kishi: Chakra is something everyone has, and it powers neat techniques by using hand signals. Blood line limits are abilities that only certain lineages can use.
Me: Ok, sounds good.
Kishi: It works like your circular system, and there's 50 60 whatever places it can be released.
Me: I can't wait to see how that's relevant some day.
Kishi: Sasuke learned this lightning move but it's not actually lightning, it's just chakra.
Me: What about the fire techniques then?
Kishi: Never mind. Cool people can do the hand signals with only one hand.
Me: Even though Kakashi, Orochimaru, The Third, and everyone else never did? Well… ok I guess.
Kishi: Rasengan is a technique that doesn't require hand signals.
Me: What makes it so special?
Kishi: Chakra is broken into 5 elements, and since Sasuke is lightning and Naruto is wind the order will be Fire > Wind > Lightning > Earth. Everything up to this point was only shape manipulation which is different and uses some no element chakra.
Me: (chokes) WTF? That makes no sense! Wind beats lightning beats earth!? So Sasuke IS lightning and not fire then? Wait, other non element techniques use hand signals so that's not even an answer!
Kishi: Never mind all that. More importantly, blood line limits are the result of fusing two elements. Yamato makes wood with water and earth while Haku makes ice with water and wind.
Me: So what about the eye techniques? They're some weird fusion too?
Kishi: Never mind. There is also light and dark chakra, which will be explained at a later date.
Me: (still waiting, I bet Kishi forgot).
Kishi: Elements can be combined to make stronger techniques, like with wind and fire.
Me: Wasn't that how blood line limits were supposed to work?
Kishi: That's different somehow. All that's required to learn eye techniques is to cut out someone's eye and use it as your own.
Me: Does that show you how to fuse two elements together to make the sharingan then?
Kishi: Never mind. There's a super powerful chakra out there that only the frogs know how to use. You sure are lucky Naruto.
Me: (tears up paper).
Naruto uses a very complex system, but it's far from intelligent. It's just poorly designed and inconsistent so I struggle to see it any other way. If I were to write all that out with One Piece's DF powers and haki, it would be a lot shorter and simpler, but it would also be well designed and highly consistent. I can't imagine how it's even a debate to be honest.
