Tennis was less stratified back then than it is now, every position below Federer and Nadal was up for grabs. For a while now you've had top 8 players consistently living up to their seedings for the most part, making it very difficult for anyone to break into the top 8. An equivalent of Djokovic would have a far tougher task of climbing up the rankings than Djokovic had at the time. Not to mention, as you claimed, Djokovic beat Federer and Nadal a few times in his big runs. Had he beaten everyone else but not Federer and Nadal, he'd not have got to #3 despite being the third best player.
So you are just supplying arguments to the fact that consistency does matter? And because these top8 live to their seeding Wawa stays out, because he does not play like a top8 consistently like they do. I just don't understand your point.
And Djokovic beating Rafa and Roger is only a consequence of his #3 level and nothing else. Wawrinka, or any other player, plays with a Top4 level for 12 months
and odds are be is #4 by the end of the year. Simple. Davydenko is a good example here as well, before Murray he was a consistent #4 and he did win MS tournaments, just like he did beat Rafa and Nole a few times.
This specific problem can be diminished by reducing the number of seeds to 16 in Slams and 8 in Masters, and by ending this 1-4 vs 13-16 and 5-8 vs 9-12 thing. It can never be fully eliminated as long as there is a seeding system though. It is wrong to believe that rankings and level of play are the same thing though, you get rankings points according to the rounds you reach in tournaments, which is not only dependent on level of play but on the draws you get and the seedings you have. For someone like say Berdych to become #1 playing better than Djokovic wouldn't be enough to do it, he'd have to play much better to pull it off since current seedings mean Djokovic will be given easier draws for the most part.
So your solution would be putting the #17th player in a bigger risk of meeting a top8 much earlier in slams? That would help him climb up the rankings?
Current seeding does give Djokovic, etc easier draws. But they got their by successfully going deeper and deeper in tournaments having much harder draws.