I don't think it's Martin having a hold at all, Farke was quite clear in his pre-match comments that Pinto isn't fully fit yet. He was cramping up after an hour against QPR. Farke doesn't expect Pinto to be properly ready until after the international break (so after Charlton in the cup and Millwall away). The same applies to Hoolahan, 2 games in 4 days was too much for them at this stage of their return from injuries.
I dare say if Pinto had played and pulled up after 20 minutes and was out for a couple of months, we'd have seen plenty of comments bemoaning Farke risking him. With the squad we have, Pinto and Hoolahan are a vital players and it makes sense to ensure they're fit for as many games as possible. Our RB/CB options are currently sufficiently limited such that if Pinto isn't available, there's no way to arrange the defence without using Martin. Hopefully as Pinto gains fitness, Klose returns from injury and the rest of the transfer window plays out, Martin will be increasingly sidelined.
Farke has said post-match that Oliveira had a groin problem and "he didn't feel good". Apparently even bringing him on as a sub was a risk. So essentially all of our changes were forced by injury/fitness concerns, Leaving the only change that is open to questioning is his decision not to let a 20 year old midfielder play 270 minutes in a week.
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I'm starting to think our fanbase would prefer our managers signed on a week-by-week contract, such is the demand for instant success. We have 11 new faces to bed in, with possibly more to follow. Half of those, plus the manager, have no experience of English football. Is it really surprising that we're not a cohesive unit yet? It needs time! Farke can't possibly know his best XI yet, and frankly I'd be surprised and worried if he thought he did. He's still learning, and he does appear to be taking things from each game.
Even this season with a sizeable parachute payment, we're nowhere near as strong financially as Boro, Sunderland, Villa, Leeds, Wolves, Wednesday, Hull, Forest, etc. If we didn't change things up, we'd have stood absolutely no chance of competing this season. This whole new set-up is a bold move from the club, to give us the best chance of promotion both on and off the pitch. Would anyone have been comfortable if we'd kept things as they were, and given Irvine or another 3rd rate British manager another £7m to spend on unnecessary wingers? Or perhaps we should have kept hold of Jacob and Howson, then re-signed Turner and Whittaker for another season because we had no money to sign anyone better?
Or would people have been more comfortable if we'd replaced Neil with some a manager from the 18th century and played brutalist hoofball? I never realised before that the league was decided in August!