This is where I come in and provide the wisdom :D
Ok, a couple of factual nuggets first and foremost that you should all digest first.
1) Alonso himself felt he had a faster car than Kimi this time. Which is quite possible especially when you go on and read number 2.
2) Kimi said his 7th gear was a little short, causing him to hit the rev limiter repeatedly, losing top end speed, making overtaking a bit tricky. He can close up on others no problem but when he wants to overtake he loses top end and can't pull through.
3) Judging by the lap times, it is clear that the Renault was definitely a match for the McLaren at Suzuka.
Now I'm sure you all know there is only a couple of obvious spots to overtake at Suzuka. The chicane and the subsequent corner into the start finish straight. Of the notable overtaking maneuvers by Alonso and Kimi, they were mostly at the start finish straight (apart from Alonso's insane move at the 130R, but we'll come back to that later). To pull off the maneuver at the start finish straight, you've got to get up close to the car in front through the 130R, into the chicane, into the final corner, get into the slip stream and then try to blast past.
Now, given Kimi's 7th gear problem, this is a bit tricky. Which is why he had problems overcoming the faster cars. Alonso didn't have this problem. Which is why he got past Webber with this maneuver no problem (except he went for the inside and nearly got pushed by Webber fully into the grass, another potentially self endangering move, but we'll come back to that later). Kimi managed to get past Fisichella's Renault mainly because Fisi made a mistake into the chicane, under pressure, he was too cautious, and compromised himself into the final corner and allowed Kimi to come right up his backside. He lacked the drive out of the corner, Kimi took the slip stream, took the outside lane, engine bouncing at the rev limiter, commited himself into taking the racing line, Fisi backed off not wanting to crash and Kimi took P1.
Why did I go to the trouble of explaining that? Because I wanted to smash the notion that the McLaren was much faster than the Renault at Suzuka. They were quite equal, this time at least.
Back to Alonso. Even after his incident with Klien and the FIA, he was still infront of Kimi. Why did Kimi manage afterwards to cover more ground to Fisi than Alonso? 2 things. Firstly, for all his spectacular overtaking and risk taking, Alonso wasn't as effective as Kimi was this time (Alonso is usually the calmer head, not this time). Kimi was patient, took his time and took full advantage of his pit strategy. Secondly, Alonso's pit strategy was less than brilliant. But then he couldn't really blame the traffic because Kimi had more of the same.
If there is any arguing that Alonso should have won, it would have been the Klien incident. But hey, shit happens. Just ask Kimi Raikkonen. If his luck was slightly better, he would have been World Champion. So, you win some, you lose some.
Ok, now the Alonso overtaking maneuver. The 130R on Schumacher was brave and commited. But also very dangerous. Alex Yoong commented that it was quite dodgy because it could easily have ended in tears. And he's right because he was off the racing line, potentially with a lot of dust a debris which could easily have taken the grip from the wheels at such a high speed, high downforce, high load corner. And Alonso would have spun out. It was a move borne of frustration, being stuck behind Schumacher for so many laps, that Alonso decided to throw caution to the wind and go for it. He pulled it off, hats off to him. And also I'd like to retract my previous statements that he isn't a real racer. He definitely is one. Alonso decided to let it all hang out, now that he has nothing to lose. Fine, but there is this thought in my mind that the previous, more calculative Alonso, would have not tried such a risky maneuver, used his brain, and tried something safer.