There is a strangely persistent idea that Pep Guardiola is not a great coach, that a great side somehow fell together beneath him for which he bears about as much responsibility for it as, say, the man who turns the lights on at the Louvre does for the Mona Lisa. He has fine players of course, but you wonder how many of them would truly prosper away from the Camp Nou. Even the greatest of them, Lionel Messi, looks a different player when he turns out for Argentina.

Barcelona are a triumph less of the players than of a philosophy, one laid down 40 years ago and refined to near-perfection in the modern era. Crucially, Guardiola is not a blind devotee. He does not simply write the same names on the team sheet and expect them to go out and do the same thing over and over again. He tinkers, revises and, like a watchful gardener, seems engaged in a constant battle against the entropic imperative.

What marks Guardiola out is his awareness of the future, not in the sense of positioning himself for a move to another club or even in terms of youth development – although he is clearly acutely aware of that – but in terms of understanding the sweep of history, of recognising that what is good now will not necessarily be good in a year or two's time. Dress it as the lesson of Bela Guttmann ("the third year is fatal") or Karl Marx ("all that is solid melts into air, all that is holy is profaned"*), but that awareness marks Guardiola as a true dynastician. Not for him the club-hopping of Guttmann or even José Mourinho: he wants to erect an edifice for the ages, something, paradoxically, strengthened by his refusal to commit to more than a 12-month rolling contract; he will not become a weary leader, governing by convention, but leaves open a perpetual route to step down for a fresher man when the occasion calls for it. (As examples from Tony Blair to Abdoulaye Wade indicate, though, leaving the door open does not necessarily mean he will still be willing to step through it when the time is right.)

In football terms, Guardiola is clearly determined to prevent Barcelona ever becoming complacent or predictable, to make sure they always have a second line of attack. The signing of Zlatan Ibrahimovic was intended to give them height, the option of going aerial if the usual tiki-taka didn't deliver and, when that didn't quite work, he began experimenting with the back three.

What is interesting about that is the way that it has changed the mindset. Barcelona often don't play a back three or a back four, but a hybrid – a back three and a half, perhaps. In the Clásico, that meant Sergio Busquets dropping deep to become an extremely deep-lying playmaker. On Tuesday, against Milan, it meant Dani Alves being given freedom to charge down the right flank, operating most of the time as an attacking midfielder. When they use a back four it is with the knowledge of a back three; when they play a back three it is with the knowledge of a four. It is neither one thing nor the other, but both simultaneously, gloriously protean and so are all but impossible to counter.

Given Milan's narrowness, the odd thing is that Alves didn't operate higher in the first leg as well, but perhaps the issue there was that Barça became a little narrow themselves. That is always the danger (admittedly not an especially big one) when Messi starts in a nominal right-sided role, as Argentina have often found; when Uruguay frustrated them in the quarter-final of the Copa América last summer after having Diego Pérez sent off, it was by vacating their left flank and trusting Messi to wander into congested areas.

The surprising introduction of Isaac Cuenca, who has started only nine league games, seemed specifically designed to ensure Barça retained their width: he is a natural winger – whereas Pedro and Christian Tello are modern wide forwards prone to cutting infield – and his value was almost entirely tactical. With Alves pushing so high that Barcelona's shape often resembled a 3-3-4, Messi and Cesc Fábregas drifting vaguely in central areas, it meant that Milan's two full-backs were kept wide, stretching the back four and so increasing the possibility of spaces opening up.

The other effect of Alves playing so high was that it took Barcelona as a whole farther up the pitch. Busquets, who so often drops in to become an additional centre-back, played in a much more orthodox holding midfield role, pushing far higher than is usual. To an extent he was able to do so because of Robinho's reluctance to track back – non-tracking forwards have been a feature of Milan for years and have arguably played some part in their exits from the Champions League in each of the past five seasons, most particularly against Manchester United in 2010.

That, of course, is something of a gamble because it means that the forward can be left free if the opponent breaks quickly, as happened when Robinho, dropping away from the defensive line, found space to initiate the move that led to Milan's equaliser (although the person most at fault for that goal, of course, was Javier Mascherano, inexplicably 10 yards deeper than his team-mates and so playing Antonio Nocerino onside as Ibrahimovic picked him out with a finely weighted through ball). It could be argued that, with a one-goal lead, Barça had no need to be playing in such an offensive way, but that would be to deny what they are and what has made them so great.

Yet while they were better than Milan and deserved winners – the ludicrous "debate" over the second penalty notwithstanding – Barça were not great on Tuesday. They were adequate. They did enough, but not a huge amount more. They could have won by much more – Messi missed two decent early chances and Christian Abbiati made an excellent save to deny Xavi in the first half – and that Milan over four games against Barça this season lost by an aggregate score of only 8-5 was largely down to greater productivity in front of goal (Barça had 67 shots in the four games, Milan only 20), but Barça were far from their most fluent, something borne out by the fact they had only 61% possession, as opposed to the 65-70% they commonly enjoy.

To an extent that is credit to Milan. Their midfield four stayed narrow, worked diligently and even, when they had the ball, caused problems as Clarence Seedorf and Nocerino attacked the space afforded them on the flanks. With Fábregas dropping back, it was effectively four on four in the middle, which, even for a side with Barcelona's close technical skills, makes for a congested game, especially when the use of a false nine denies them the option of bypassing the midfield by going long. Hércules, similarly, played a flattened midfield diamond when, 53 games ago, they were the last side to beat Barça at the Camp Nou.

Fatigue, physical and mental, may be a factor – which must be a concern for Spain in the summer – but it's important to keep these things in context. Barcelona have beaten a decent Milan side 3-1 on aggregate with barely a scare; it's a measure of how good they are, how high expectations, that that should bring a slight sense of disappointment.

Yet for Guardiola the relative lack of fluency must be troublesome. Is it a blip, the sort that is inevitable, or is it an indicator of longer-term decay? An awareness of entropy and putting in place measures to combat it is one thing; winning that battle is something else.

*Given that Marx categorised the "bourgeois epoch" as being distinguished by "everlasting uncertainty and agitation", you wonder if that epoch has found its apogee in modern football.