I think deep inside you already know the answer. Because current matchup algorithm is just a bad idea, most people don't need any other arguments except statistics and common sense.
As for other "quit reasons" you've mentioned, they speak about Inno decision makers' immaturity. Which should raise some red flag on its own, but it's something that can (at least theoretically) be argued with. I haven't heard a single argument in favour of GBG matchup algo. That counts for something, right?
Well, if you take Lorien's (sorry if I have mis-spelled) example, you will see a guild that has 2 homes, Project Phoenix (aka PP) and Project Phoenix 2 (aka PP2) - most certainly these 2 (which are basically one) are more than happy with the current GbG matchup, as it allows them to control the map basically every single round. Another strong guild known as Kamikazee Penguins, on their own, could be a match for either PP or PP2, but with these 2 nearly always together, the Penguins also get dominated. So, by taking this ID type algorithm and create 2 (or more guilds) and build them both up, then they should theoretically be able to control the entire GbG every single time. And if you look at the guild members, you will see what are undoubtedly duplicate accounts (against TOS of course), allowing them to participate in both of these twinned guilds.
So, from this point of view, very favorable matchups. And those players with duplicate members in the other guild, will stay unchallenged by Inno, thereby creating yet another method and reason why it is difficult to believe that anyone is going to create any meaningful change - or at least enforce the supposed rules.