From a design perspective, I am not a huge fan of the second hour/unlimited life thing in general as it feels less FSO-like, but I feel like it's necessity now. Plus, if it allows more people the ability to enjoy my design more in-depth than they would with just 1 life, I think that's a positive.
For me personally, my main thing is that one side cannot/should not be able to pull a 'come from behind' win due to Hour 2 lives for the exact reasons you state. We lose people, sides may get imbalanced, there is no commitment to stay for Hour 2, etc. For what it is worth, my Hour 2 designs tend to be simple off-shoots of Hour 1, with whatever the objective is being the same or close by as Hour 1, as to not require an entirely separate plan. I feel the goal of Hour 2 should be to have fun, eg. if a squad gets 'bomber duty' in the first hour, they should not be obligated to have to do the same in the second sortie.
My 2 cents.