One thing I'd like to add to the President discussion. We've seen minor changes in the MCU from our universe. Dates and days of the week have been different. It's entirely possible that, for some reason, the Presidential election cycle is different than in ours. Perhaps it's off by 2 years, so Obama was President from 06-10, Ellis was elected and took office in 2011. It's also possible the terms are different, maybe only 3 year terms.
Alternately, I could see Obama getting elected in 08 and stepping down or being impeached in 12 after the Battle of New York. Ellis was the first acceptable person in line, and was the acting President after, and had just successfully been reelected in IM3.
There's a bunch of possible explanations, but without further information we can't really come to a solid solution.