Thanks for linking to that ELO site, very interesting. Of course there is no such thing as a perfect system for ranking teams, and people are free to point out where there may be errors or mistakes in their approach, but just saying 'that ranking is sh*t because Team X or Team Y aren't in the top 5' is a bit silly. Ask people to name the best English side of the last 25 years and the Man Utd treble winning team or the Arsenal Invincibles will probably top many people's lists. Yet that Utd team only managed 79 points in winning the title, and the Arsenal team drew a huge number of games in their unbeaten run. I'd take Mourinho's Chelsea team (first spell), Guardiola's City team (100 points), and this season's Liverpool team over both of them.
There are things I agree with and things I disagree with here. First, you have this a bit backwards. History happens, people form opinions, and then models are created to explain said history. It's not the other way around, it's not a model that came first to tell us Team X or Team Y is great. Secondly, comparing teams for points, wins, or whatever other metric assumes that those conditions remain unchanged. That's not the case. You can start tweaking "league strength" coefficients, but then you'd be introducing more bias in the model. Therefore, I still stand by the statement that if the model does not meet accepted checks, it's a shit model.
But what you said about the teams above is not very wrong (IMHO), except for the Chelsea team perhaps. The United Treble, Arsenal Invincible and Pep's last two-seasons team are right up there. (*personal bias on*) But we are better than all of these. Ultimately, those teams that are talked for a long time after they are gone are the greatest, and I think that we are up there. I actually think our achievement this season does take some gloss off Pep's team because it happened too soon afterwards.
As for Carra and Keane, you have to consider that they played with their mates for a long time. That's the definition of a personal bias, isn't it? Plus, Keane saying all the time that he has to be loyal to his buddies...
I mean, Schmeichel in goal instead of Alisson? Well, he's been there for many years, Ali has been here for two. Let's talk again in a decade. I don't think Ali will be much better then (can't see how much better can one get), but he'd have been here longer. Same for Trent, maybe Gomez too. What I'm trying to say is that with players of the present quality of Ali and Trent would have definitely made the "team" had they had playing for longer. But these teams are nonsense anyway...