Based on the manga by Nakamura Nishiki.

Which anime main character has the least cliches?

In my opinion, him: Dan Kuso, from Bakugan. Now, what makes him not be a very cliche anime character? His parents are alive, BOTH of them.
Neither of them are absent in his life.
They live at their house and live as a normal family. His father is also not a legendary hero or anything of the sort.
He is a simple business man who shows up now and then at his house looking for pudding.
He is absolutely invisible to the plot and the most outstanding things he did was get transferred to a different city in his job which led to season 3 and 4 being set in a different city as that in season 1 and 2 (regardless, he was pretty much forgotten post season 2).
He could have been completely absent the entire anime and I doubt anyone would miss him.
My theory is that the reason he exist is to make the point Dan has a present father and that his parents are married. His mother is no legendary hero either.
She’s a typical housewife that is seen doing yoga now and then.
As opposed to her husband, she was pretty useful to an extent, for instance, her interference leads us to learn about the fate of the character in an episode without actually seeing it first hand. Ex 18:30–17:00: In this same episode, also she inspired some character development. But aside from that, she is only show a handful of times later on.
If she or her husband were killed at any point in the series, Dan got over it extremely quickly and it didn’t affect him at all. This is opposed to most (if not all) anime I watched to date, in which the parents were either dead or couldn’t be with their children for whatever reasons. Another thing is that he is not glutton. Most main anime characters we see east A LOT.
Goku, Luffy, Naruto, you name him! He can eat all the food in a feast and not get fat at the slightest.
Dan on the other hand has never shown to have devoured an entire table all by himself. After season 3, he is never beaten by his Tsunandere. Personally, my vote goes to Dan as the least cliche anime main character.