I would hardly say Mottram was "fresh" at the end of the season. He nearly withdrew from the race because he felt so tired and stale from a regular season of racing since April.
Nor did he get "toasted" at the CWG- the 5000 was a great race that he lost, but it's not like he tanked horribly. It was a great race that he didn't win, big deal. The 1500, he fell, which happens to even the best runners- ask Jim Ryun or Mary Decker about that.
Finally, Bekele ALWAYS has an excuse when he gets beat. The fact is, he seems to have some trouble running tactical 5000 meter races-- his last 100 meters doesn't seem to match up with an El G, Kipchoge, etc (basically, guys with insane 1500 speed). A 10K last lap in 53 and last 1000 in 2:28 will smoke almost anyone, but a 5k that closes in like 1:52 seem just a little quick for bekele.