Re: Will 2008AO~2009Rome end up Nadal's best run in his career?
No. After the 2008 AO, he won Roland Garros, Wimbledon, and the 2009 Australian Open, as well as Monte Carlo, Hamburg, Canada, Indian Wells, Monte Carlo again, and Rome, not to mention the Olympics. That's 3 out of 4 slams as well as 6 out of 11 Masters Series titles and an Olympic Gold Medal.
No matter how good you are, you nee to also be a little lucky to dominate that much. I suspect Nadal will never manage to do QUITE that well again, but I suspect he will play as well as before. He just might not manage to be THAT dominant.