Very good question after the 2:01:09.
Pro Bekele: Insane track career, XC and insane Marathon PR.
Pro Kipchoge: Longvity and neverseen domination in the marathon for 10 freakin' years.
I'd still go with Bekele. Yes, he flamed out quicker, but this has to be expected and the "best" doesn't mean very good for a couple years, it means the best, the quickest.
Medals/titles: Bekele wins.
PRs: Bekele wins, too. 12:37/26:17/2:01:41 in total looks better than 12:46/26:53/2:01:09.
When Kipchoge threepeats it might change.
Until he does that, it just shows how absurd good Bekele was, as he ran close to Kipchoge's marathon WR although he wasn't at 100 % anymore and barely able to string together healthy training for a long period.
My thesis: If Bekele started running marathons in 2009, he for sure could have run at least 2:00:xx.
So in short: Better overall runner at peak: Bekele.
Better longvity and road racer: Kipchoge.