RotS Yoda >>> TPM Yoda?
There are several quotes putting both RotS Windu as a peer of RotS Yoda, and TPM Windu as a peer of TPM Yoda. It seems pretty likely that Mace Windu grows considerably between TPM and RotS - he was still relatively young, mastered vapaad in that timeframe, and is implied in more than one TCW-era book to still be growing in power. Unless if Windu mysteriously stagnates, it seems more likely than not that Yoda would have had to improve as well. This would also explain why Dooku thinks he can defeat Yoda in AotC, and indeed did better than one would expect, yet is terrified of Sidious and never entertains the idea he could win 1-1. Dooku as of TPM is also implied to be within the same general league of Mace and Yoda as a pure duelist.
Given that Windu IIRC said sometime around TPM that Yoda had slowed down a little, it seems possible that the events leading up to RotS inspired Yoda to pick up his game and shake off the rust, and/or that his spiritual journey in TCW really boosted his power.