I see that most people are disappointed with Arc V’s ending.
I’m not going to try to tell you that you’re wrong for feeling the way that you do, but I’m going to propose that you look at it from another angle.
Arc V was a story of consequence.
DM, GX, 5Ds and Zexal all had more than one antagonist. Sometimes their goals would overlap, and the actions of the lesser antagonists often inadvertently helped the Big Bad. But for the most part, all of the antags had their own goals. The end result of this was that often, the carnage caused by the lesser antags would often be reset in some way, done away with immediately so that the main characters could take on the next antag without any major baggage.
Arc V only had two antagonists, Leo and Zarc. One of Leo’s main goals was to stop Zarc’s revival, which he viewed as inevitable. We can infer that if he had any sentience within the boys, Zarc hated Leo in turn for seeking to revive Ray. Their goals were antithetical to each other.
However, Zarc only became a truly destructive factor at the very end, for what, an hour or two in-universe time? On the other hand, Leo’s been at it for at least 10 years (we know that because of Jean Michel). And what did he do during that time?
He turned Academia into a military school churning out child soldiers. Through Jean Michel, he exacerbated the class divide in The City. He utterly destroyed Heartland. He ripped the bracelet girls away from their families, away from the people who loved and cared for them. He put the Yu boys through the wringer, enabling Zarc to influence his fragments towards each other.
Realistically, none of the above can be easily undone. If ever.
We can assume that Academia is no longer a military school, but we can also assume that the brainwashing the students went through is still in effect; that sort of conditioning takes years to overcome. Not every student there is like Sora, or Asuka, or Serena; not all of them had the capacity to break out of the ‘soldier’ mindset on their own.
The City was explicitly said to have gotten better after Jean Michel’s demise. But better doesn’t mean perfect, and I’m sure the divide between the classes still exists—at best, security is now more reasonable, and the class gap is now a bit smaller.
We know that Heartland is still in ruins, and that it’s citizens are still traumatized. That sort of destruction takes generations to amend, but the legacy of the genocide will always exist. That sort of thing just never goes away.
Save for the problems of the City being a bit too easily overcome, for the most part i think that the fandom was fine with the above three. Now, for the more controversial consequences?
Serena, Rin, and Ruri are now a permanent part of Yuzu; Yuri, Yugo and Yuto are now a part of Yuya, forever. They will presumably go on to exist, and we can say that Yuya and Yuzu will both be able to communicate with their counterparts at will. But six of the eight counterparts are now without bodies.
That’s heartbreaking, when you really think about it.
Ruri and Yuto had an entire group of friends that will never be able to see them again; Shun has lost his hometown, his sister, and his best friend, permanently.
Yugo and Rin’s dream of rising out of Commons through their own skill, side by side, will never truly be realized.
Serena spent her entire life confined behind Academia’s walls, and now she will live out her existence confined in Yuzu’s consciousness. And we never truly got to know Yuri, and what his aspirations were outside of ~having fun~; but him never getting a proper redemption arc is something to be mourned in and of itself.
And that is a consequence of the war, one that cannot be undone. The counterparts merging permanently is a painful reminder that the effects of war sometimes never go away. You can interpret Serena, Ruri, Rin, Yuto, Yugo, and Yuri as casualties in the interdimensional war. And just like in the real world, people don’t just come back from the dead because you love and miss them and wish they could come back.
I take solace in the fact that Yuya is now stronger for the presence of his counterparts. We can presume that Yuzu is as well. The six other counterparts aren’t gone, they simply… took a different form. Just as you can say the people you love never really leave you.
Consequence. I’d count this bittersweet ending as the most profound we’ve ever gotten out of a YGO spinoff.