It’s not surprising if Marvel was playing with several different ideas regarding what to do with different characters in Phase Two.
Bringing all the main heroes together with The Avengers was a feat unto itself at the time that nobody was quite sure was going to work, likely including the folks at Marvel themselves.
Iron Man 3 was the first film in Marvel’s Phase Two, so it sounds like this conversation Joe Robert Cole describes to Complex was probably happening around the end of Phase One.
While that film set up a place for the characters to go, which has led us to Avengers: Infinity War later this year, they likely hadn’t put a great deal of work into the details, for the simple reason that if The Avengers didn’t work, the rest might not happen at all.