I personally thought Walker was the saving grace of the third film (that and the so-bad-it's-good line "Help I'm a turtle and I can't get up!). He was a fun villain and gets a falling death scene as well (though with bad effects, implosion anyone?). I haven't seen much of Sh'Okanabo yet other than his death scene which looks really cool. Since 2012 will be "the definitive TMNT" for me with all the classic characters, when I watch the 2003 series I'll not expect the same, and appreciate it for everything it is.
But, one thing they both have in common: Neither appeared in the 1987 TV series, being original to TMNT III and TMNT 2003, neither of which had its own Krang (unless you count Utrom Shredder, whose real name is Ch'rell), and the former didn't have a Baxter Stockman either. Both are also set in a distant time period (ancient Japan for Walker, 100 years in the future for Sh'Okanabo).
Of course AVGN criticized the third film for Walker and Norinaga being its villains instead of Krang, Baxter Stockman, the Rat King, or Leatherhead (why Leatherhead? His second personality is more hotheaded than Raph but he's not evil. What's wrong with Lord Dregg? Or was he not in it yet by the time of this film?), and the fact that it was set in Ancient Japan, and one could say the same for Sh'Okanabo.
Did you like them as villains and not mind them being original characters to their respective universes? Or did you dislike that they started making their own characters instead of using Krang or other villains not yet seen in them?