Ursegor
World Champion
More to the point, if a system involving Javi at CB is adopted, (which is not at all unrealistic, we can argue about its merits some other time) it's quite likely that Thiago will get a lot of minutes and may become a part of Pep's 'ideal XI' . They have a stacked squad and I'm sure anyone could come up with plenty of good looking lineups that don't involve Thiago, but that fact hardly shows that he is now doomed to warm the bench.
If Javi stays in midfield though, it'll be with Schweinsteiger and Thiago finds himself competing with Kroos/Muller/Gotze for two spots, and that's assuming Ribery + Robben is still a permanent fixture, which I don't think is a certainty.
Basically ou have to assume Javi won't play CB, Ribery and Robben will both start all the time, and Gustavo/Kroos/Muller/Gotze are all certain to be higher in the pecking order than Thiago in order to conclude that he's definitely going to be starved for minutes.
It's confirmed that Bayern will get Lewandowski next summer. This reduces the chances of a false 9 system so in CAM Thiago will compete with Götze, Müller, Kroos and in CM he will compete with Schweinsteiger and Kroos, even if Martinez is forced into a CB role. Which, by the way, would be stupid to begin with. Schweinsteiger is not a holding midfielder. They don't have another holding midfielder of Martinez' class, which is why they paid € 40M for him in the first place last summer.
But then again Pep never had a clue in the transfer market anyway, so, yeah.