I used to use an Eglu Classic and I thought the ventilation was less than perfect, though my girls didn't have respiratory problems as I used to leave the pophole open. Do you close it up at night? i know that in the cube you can close it part way if the run is safe - my friend does this with his Cube. I gather from your other post that you had respiratory problems in your flock, so lack of ventilation might have made these worse, rather than caused them, do you think? There's a long thread going ATM 'Condensation in coops' where people are discussing ventilation problems, and we've been hoping an Omlet owner will contribute experience.
Also, in the Omlet houses, I would prefer proper perches - when I got my new house with 'real' perches it was so much easier to keep clean than the slatted bases in both sorts of Omlet houses.
Have you looked at the thread 'Rat? problem,' where a chicken was killed presumably by a small predator getting in through the drainage hole at the base of the moulded nestbox? Not a worry with the Cube as it's so much higher off the ground.