You make fair points.
1. I watched the fight again earlier and I didn't see any strike that looked like it could have affected his cardio that badly. It did look like he had an adrenaline dump (McGregor too to an extent) and that didn't help. Even being in shape like Mendes was, being ready for a 5 round fight like this on two weeks notice will affect his cardio. I think many things factored into his gassing.
2. You're right. I'm sure he didn't spend a ton of time on takedown defense preparing for Aldo. McGregor could have prepared better for a wrestler with more time, but preparing for a wrestler like Mendes would take years of training. McGregor seems like the type of athlete who can adapt, it'll just take time. This fight could end up being a great lesson for Conor. He'll be more likely to get his wrestling on point, because he sees what can happen against an elite wrestler, even a gassed one.