Limo has a chance to be better.
Here are their 6 fastest races (1st number is performance rank) and results:
.3 2:05:38 Khalid Khannouchi 1 London 14.04.2002
.4 2:05:42 Khalid Khannouchi 1 Chicago 24.10.1999
.7 2:05:56 Khalid Khannouchi 1 Chicago 13.10.2002
.9 2:06:14 Felix Limo 1 Rotterdam 04.04.2004
25 2:06:39 Felix Limo 1 London 23.04.2006
28 2:06:42 Felix Limo 2 Amsterdam 19.10.2003
29 2:06:44 Felix Limo 1 Berlin 26.09.2004
53 2:07:01 Khalid Khannouchi 1 Chicago 22.10.2000
54 2:07:02 Felix Limo 1 Chicago 09.10.2005
58 2:07:04 Khalid Khannouchi 4 London 23.04.2006
67 2:07:10 Khalid Khannouchi 1 Chicago 19.10.1997
425 2:09:01 Felix Limo 3 Rotterdam 10.04.2005
Definitely, KK has won more of the bigger races, both London and Chicago '02 being the biggest, and 5 of his 6 fastest times yielded wins, so qualitatively he has the edge over most anyone, but Limo is young (25), and has a good chance of racking up many more big wins.
Amazingly, KK ran his 5th fastest career time Sunday.