So when we are looking at a completely full list and seeing who are clear best 22 when fit:
Essendon: Goddard, Myers, Ryder, Bellchambers, Fletcher, Dempsey, Chapman.
Fremantle: Fyfe, Barlow, Walters, Mayne.
Then you go to the fringe/depth players who were injured:
Essendon: Pears, Kommer, Ambrose.
Freo: Bradley, Gumby, Ibbotson.
No doubt Essendon struggled with personnel ... but you are not making a fair comparison. Ibbotson was in AA form last year before injury, he is clearly best 22.
I would imagine that Sylvia and Morabito will be inclusions by the end of the year. They're just not ready at the moment. It is definitely a stretch to say they are important outs seeing as they basically haven't played under Lyon, but at the same time they could be important inclusions.
You should add Mundy as well, if you are going to include Goddard.
This makes it:
Essendon: Goddard, Myers, Ryder, Bellchambers, Fletcher, Dempsey, Chapman.
Fremantle: Fyfe, Barlow, Walters, Mayne, Mundy, Sylvia, Morabito
This includes 5 players from our top 10 in the 2013 B&F. Whereas Essendon were missing only one.
At the end of the day, the result is fairly meaningless considering both sides had significant outs, but I would look to the heat/travel/gastro as better excuses than the injury list.