I love the original (: and season zero is really good, too. I'm in the process of re-watching all of them
The original. Definitely.
Each series with the exception of the first series which was relatively bad either way, has it's ups and downs. And with such, each series also has it's variety of reasons why I make this opinion. Let's look at the main values as stated by each of the series, in relatively simple terms.
The millennium puzzle, as represented in Japan, was merely a tool used to receive what is considered a "destiny draw" which translates to stacking. The main concept of the original series was in the depth of actual gamplay that cheaters will always prevail. This is why I don't really like the representation of the original series.
Now let us take a look at all the varied items of importance in the plot of GX. The first two seasons were pretty simply the concept of a kid defeating all odds and having fun doing it, a great moral lesson. Although the true values start in season 3, in which the supreme king and Yubel begin having an influence in his life. The concept of the supreme king was a beautiful representation of the fact that one cannot simply be good in a pure sense, and in everyone rests an evil weakness. This is what embodies the concept of the supreme king. And in turn, Yubel represents the split in personality that breaks it down to the concept "We are all evil heroes." This is probably my second favorite series in morals, yet my favorite in plot. They went all over the place with this series, and I loved it.
Now, 5D's. Before everyone starts yelling CARD GAMES ON MOTORCYCLES, let's look at the real ideas of the series. The majority of the main characters are represented as basic scum, outcasts, and "not good people." Crow is essentially a robin hood, jack is a thief and a double crosser, Akiza is basically a science experiment. The only non-outcast types are leo and luna, who might as well have been since they pretty much don't have parents the entire series. And yet they all come together and save the world, and unite the slums and the city as one. The best moral story in the end, and borders the concepts of the civil rights movement. But now i say... motorcycle duels? REALLY. That's why it's not my favorite in plot.
I haven't seen enough of ZeXal to have an opinion, so I'll leave that out of my review and opinion. :3
for me it's GX i think the main reason for this is the school setting and main character though i haven't seen 5D i have seen Yu-Gi-Oh! 3D bonds of time and Yusei seems abit reserved and too serious for me and i have no problem with Yugi he just doesn't seem to stand out for me.