Average strength (along with nukes) is a large percentage of combat effectiveness. The nations arrayed against Legion had a much greater number of nukes and a higher average Nation Strength. Therefore, the superior numbers and Nation Strength of the Legion were offset by the fact that Vanguard et all vastly outnumbered Legion in the top tiers.
It's not so much of a lack of preparation for nuclear warfare (although there was some of that too) as a lack of an ability to buy nukes because of a lower average NS. Since Vanguard and allies primarily targeted Legion (PAIN and Universalis did, at least, don't recall whether Vanguard did), we were the recipient of most of the nukes and most of the damage. While the damage dealt by Legion and allies was just about averaged between Van/Uni/PAIN, the damage to Legion/UPN/Invicta/Elysium was mostly concentrated in Legion. One could say that this is because Legion are incompetent fighters, but I'd argue that it's more to do with the large numbers of nukes that we took and the fact that Legion was outnumbered in the top tiers.
Just a little disclaimer here: Your points are certainly valid and I respect you for them. I like it alot when people trash Legion and actually use facts to back it up, as it can generate a fun and healthy debate.
EDIT: Do you happen to have the numbers of nukes received by the various engaged alliances?