Wholeheartedly agree. The fact that he played in Death Valley while Youk plays in hitter's heaven should not be understated. The statistics back it up too.
On to the topic of lineup construction, i am a firm advocate of an Ellsbury-Crawford-Pedroia 1-2-3 with Gonzales hitting fourth and Youkilis fifth. I think you could make the case that because of his insane contact abilities, and the power surge he was showing last year, he could be considered the "best" overall hitter on the team, and having him bat third would, because of that, make sense.
Also, the idea of Drew leading off doesn't seem particularly necessary with Ellsbury hitting like his life depends on it since the beginning of Spring Training and how much Drew lengthens the lineup when hitting at the bottom of it.
My ideal lineup:
Ellsbury
Crawford
Pedroia
Gonzales
Youkilis
Ortiz
Saltalamacchia
Drew
Scutaro