No one judges the greats in friendlies or qualifiers. Messi's 0 for 7 in the games the greats are judged in.
You have to take into account the era he is playing in.
To start, Messi is not a pure midfielder so he cannot control a game like Zidane did in 06 against Brazil. He will see the ball, but Biglia, Benega, Mascherano and Di Maria will get more than there fair share as well. He plays as a forward after a long season (a player who plays more games than anyone) with almost 2-5 players permanatly glued to him throughout the game, like a lot of other star forwards in knock-out stages.
Which leads to my next question, when was the last time a group of star forwards completely dominated any entire international tournament from start to finish? 2002 World Cup, Ronaldo, Rivaldo, Dinho and 2004 Copa America with Fabiano and Adriano (a last gasp from a bygone era). Since? Nothing in any Copa America, Euro, or World Cup. There is absolutely a delineation, a shift, pre-2002 and post-2002. Closest is Torres and Villa in 08 but they still needed help. Before 02 Pele, Garrincha, Platini, Van Basten, Rossi, Maradona & Valdano, Romario & Bebeto, Henery & Trezeguet were dominating year after year. Now nothing for going on 16 years. It just doesn't happen anymore.
Euro 2004 happened, Instanbul happened, Porto happened. Mourinho and Rafa shifting the popular trends in tactics. Low block defending, focused on maximizing athletic abilities, tall centerbacks and beastly defensive midfielders, dark arts became the norm. And now over a dozen teams in Europe, South America and Africa have the formula. Of course a system can be created to break them down but not really for national teams due to lack of time.
If you see the teams that make the final or win these tournaments a pattern becomes clear. No forward dominates all those knockout games, depth is king. Every single one of them needed a goal from a player who isn't a forward who scores regularly for their club. Think goals from Puyol, Hummels, Álvaro Pereira, Alba, Xavi, Pirlo Silva, Alonso, Schweinsteiger, Payet, Grosso, Materazzi, Van Bronckhorst, Isla, Vidal Sneijder, Eder, Zidane, Iniesta etc. Knockout stage or difficult group games in June and July are too mentally exhaustive these days for ANY forward across the globe who scored regular club goals (18+) to take over and dominate every game. It's too scrappy where physical strength and unpredictably trumps pure skill and speed. Where mentally exhausted forwards are drained even further. And Argentina themselves do not score enough of those goals to actually win.
Now we get to the issue of Messi himself. Other than a game against Mexico, all of those knock-out games were against tight, discplined physically strong defenses. Messi is a freak footballer, but he's not a freak athlete. He is fast but not clearly faster than everyone else and certainly not stronger. Would a freak athlete footballer like Ronaldo do better in this era? There have been other more stronger and athletic strikers during this time. Gerrard, Rooney, Drogba, Suarez, he who fannies about and dives around, Klose, Pogba were all shutdown, or at least didn't dominate, at this stage for one reason or another when they faced an atheltic and discplined defence. Ronaldo and Dinho themselves couldn't beat France in 06. This is with all the modern training and diet forwards get and the preferential treatment from refs. The exception that sticks in my mind is Balo against a strong Germany in Euro 2012, but there are one-offs for everything. Thus Messi not being an incredible athlete isn't really a huge issue. And of course if the likes of Suarez can get shut-down than I don't think it's a mental issue either.
TL:DR, I don't think there is a forward in the history of the game that would dominate those games in this era based on your criteria. The defenders across multiple teams are too athletic and well trained, the forwards can't build chemistry and they are at the end of longer, difficult seasons. Goalies are too strong. Defense is easier to improvise. And thus scrappy, unexpected goals from midfielders, defenders and back-up strikers are the norm. Messi is none of those things.
He's not a master of scrappy goals. But those people don't win the majority of games like he does. Scrappy goalscorers are going to miss most of the time and can be out-scrapped by anyone at any given time. Headed goals, freekicks and screamers from midfield simply aren't as reliable except at the very end of international tournaments. But they don't get to knockout stages without players like Messi.
