Dear OP, why was it so popular? I can't speak for every AkuRoku shipper, and
I second a lot of what's been said in the other posts, but I feel like there are elements missing in these discussions to understand the love for these two characters together.
Here's my case: Chapter 19 of
Boys by Casey V, "Interstate love song" (written in 2008)
An Archive of Our Own, a project of the Organization for Transformative Works
archiveofourown.org
It's one chapter (12,000 words) that works as a standalone piece within a much bigger story of (soriku) teenage romance in the midst of high-school homophobia in the 1990s. It's an alternate universe: small town in Oregon, in which Roxas is a Nirvana fan (and 1994 happens), Axel is one year older than him (that's it--one year) and a Black Sabbath fan with spikes on his wrists, Larxene, Zexion and Demyx are the other members of their little gang who hang out at the skatepark and smoke way too much way too young and all kinds of stuff. Apart from the excessive recreational drug use, it's a pretty safe read and I totally recommend it for a blast of emo/1990s nostalgia. Sex happens, but it's like a couple of lines near the end and all perfectly age appropriate at that point. Slippery slopes of consent happen, but they are dealt with and no lines are crossed. Zero traces of the Soriku main story in this chapter. It really is just a massive tribute to the Nirvana generation.
So that's my light-hearted response
I think the characterization in this side-ship sums up the appeal pretty well.
Now the rambling, less cute thoughts.
Of course, this is blissfully ignoring the fanworks influenced by the harmful seme/uke dynamic, if not worse (chan), which have put me off the ship even before ""canon ages"" burst the rose-tinted bubble. I'm happy to focus on how there have always been beautiful stuff like Casey's Boys out there on the internet, which did address the relevant issues while focusing on hope and love. And given how popular this particular story is--it's the Kingdom Hearts story with the most likes and bookmarks on AO3, of all times, of all ships and non-ships--, maybe it gives some idea about how not-totally-messed-up the so-called "rabid yaoi shippers" are. It also shows how much shipping is about taking what clicks for you in two or more characters from canon and throwing away the rest.
I'm not a fan of what canon has set up for these two characters, so I can't say I ship them beyond that one aforementioned AU I read that was great and resonated with my own experiences of dating an older guy as a teen. I am RELIEVED that people are coming to their senses and pointing out issues of consent and power imbalance more and more. Fanworks are much healthier today than they used to be (queer media, too). However I can't say I'm a huge fan of the shaming the AkuRoku shippers (and all problematic non-canon ships in general, in any fandom) are getting these days. These ships need to be explored in a safe space (=> amateur writing, not reality, underground, words, very marginal impact) and by making the ship taboo, we're not giving them one.[/SPOILERS]