Well, bubble screens are rarely used in the NFL to replace running games. They are used in spread offenses in the NCAA, with Oklahoma State, Kansas State and Baylor, etc... as running games. Very few NFL teams use the bubble screen more than 3-4 times a game. Oklahoma State will throw the bubble screen 15-20 times a game. If an NFL team threw 20 bubble screens, I would agree with you that it would be a major cause for concern.
That being said... the Patriots use intermediate passes to Welker, Hernandez & Gronkowski to partially replace the running game that they lack. But the sure handed nature of those 3 receivers combined with the accuracy of Brady makes it work in New England. There isnt another team in the NFL that can say they have those elements.
I don't know why New Orleans drafted a RB with their 1st round pick. I wasn't privy to their discussions prior to taking Mark Ingram. Maybe they thought he was the best player available regardless of position? I dont know. Maybe they thought they had a huge problem. Again... I dont know.
You said that if New Orleans and Indy could effectively run the ball, being up by 10 and then running the ball wouldn't hurt them like it does now. I agree 100% That is a no-brainer. However if they didn't utilize the strength of their passing game and take advantage of having Drew Brees and Peyton Manning like they have done, I would think that they would be up by 10 points late in the 4th quarter much less often.