The two names you hear at QB for the upcoming draft are Sam Bradford and Matt Stafford. Only one of these names is a viable option for the #3 overall pick. I'll tell you which one and why.
None of the elite QBs in the NFL completed below 60% in college. Peyton Manning and Tom Brady completed 63% and 62% respectively. This year's rookie standouts, Matt Ryan and Joe Flacco, were 61% and 63% respectively.
This isn't to say that all college QBs with a high completion percentage are good NFL QBs; see Alex Smith (66%). But, notable underachievers Joey Harrington, Cade McNown, and Ryan Leaf all had completion percentages below 60 in college. The only decent NFL QBs with college completion percentages below 60 were Carson Palmer (59%) and Jay Cutler (though I'm not quite convinced that he is decent).
Matt Stafford has only completed about 57% of his passes in college. Sam Bradford has completed 69%.
Sam Bradford is the only option at QB worth the #3 overall pick. If Bradford is gone by then, the worst thing the Chiefs can do is reach for another QB. The Chiefs would be better off drafting another need position, either on the offensive line, or any of the front 7 on Defense.
The Chiefs probably do eventually need a first round QB; 9 of the 12 teams in the playoffs this year have QBs that were 1st rounders (By the way, 8 out of 9 of these QBs had a completion percentage over 60% in college, with Kerry Collins as the only exception). But, I think it is reasonable to give Tyler Thigpen one more year if Bradford isn't available.
Once upon a time, the Chiefs had a mobile QB that needed a little improvement. His name was Rich Gannon. Keeping Thigpen around to develop isn't the worst thing that could happen to Kansas City.
There is a lot more to evaluating a QB than just completion percentage, but it is a pretty good place to start. Stafford may turn out great, but probably not. Whoever the Chiefs draft at #3, they need to be 100% sure that they will be able to contribute in 2009.