Yes, I mostly agree. It would be great if the coaching staff can come up with methods to lengthen Messis' peak stage of his career. Also, I'd like to contribute a bit as well.
I definitely agree that Messi won't be able to cover big distances when he gets closer and beyond the 30 mark, . Keeping that in mind and the fact that defensive work required by the midfielders is immense, why not play Alexis up top instead of Villa? This way Messi and Alexis can switch their positions depending on whether Barca has the ball or not. It would also work since Alexis can play very well in midfield, only to the point where he switches back with Messi, though. (Having said that, hope Alexis integrates fully and quickly because I know he can do it.
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The other potential candidate for Messis' current position could be Cesc. This way the alternating roles mentioned in the previous point could be expanded with Cesc and Messi swapping positions to add variations to the build-up.
The role of the wide forwards wouldn't change much which is to provide width and work in the channels. So, in your line-up I'd shift Villa out wide and replace him with Cesc/Alexis. As for the other midfielder, Xavi would be my first choice but I feel that Iniesta could play his role well. He's fully aware of how to control the tempo and build up plays and, apart from that, could also allow Messi to play in a 'central right' role because that's the space where he often drops into when he's playing as a false nine. Let's not forget Thiago either.
Also, I've thinking about it and I haven't given up completely on the three-man defence. Didn't we concede less goals than Madrid last season? Was it in the league only if that's the case? I'm not really sure but I'd like to give it another go. Something like this (Assuming Messi plays deeper, that is.):
Bartra - Pique - Adriano/Puyol
Mascherano
Busquets - Xavi/Thiago
Messi
Pedro/Cuenca - Cesc/Alexis - Villa/Tello/Iniesta
With Mascherano sitting just in front of the defence during possession in the oppositions' half. This way he can do what he's been doing for almost his entire career ( may help against the counter as well ) and then drop back into defence resulting in midfield of Busi-Xavi-Cesc with Messi switching positions.
This is just a thought, though. With the players being so versatile, there could be numerous changes and systems.
And with Tito being the coach, the positive thing is that the team isn't focused on being fixated to one style and will be able to make minor tweaks should it required by the situation.