...Unless we assume that Mendez that day was feeling the weight of his own years particularly heavily, and thus thought that the somewhat graying Pike of STXI and the somewhat balding Kirk of "The Menagerie" both fell in the same age pigeonhole, two steps below the depressed (but well preserved) Commodore himself. 
As far as the "altered timeline" thing goes, we can assume that everything that precedes Nero's first attempt at interference would stay the same between the two timelines. Thus, Pike and Kirk's relative ages would supposedly remain the same, even if their later joint history went differently from how Ziggy remembers it. And it does seem that this could be the case, at least if we squint a little - so no minus points to Abrams for that, yet.
Just as a side note, the dialogue in "The Menagerie" has the predominant characteristic of being very clipped - from the part of Mendez, apparently because he is so bothered by what he knows of Pike's fate and condition, and from the part of Kirk, probably because he catches on to the strange mood of the Commodore. Thus, even though the phrasing might suggest that Kirk only met Pike once before and didn't really know him, we don't need to follow that suggestion: hints at a longer relationship would be erased by the terse tone of the discussion.
Timo Saloniemi

As far as the "altered timeline" thing goes, we can assume that everything that precedes Nero's first attempt at interference would stay the same between the two timelines. Thus, Pike and Kirk's relative ages would supposedly remain the same, even if their later joint history went differently from how Ziggy remembers it. And it does seem that this could be the case, at least if we squint a little - so no minus points to Abrams for that, yet.
Just as a side note, the dialogue in "The Menagerie" has the predominant characteristic of being very clipped - from the part of Mendez, apparently because he is so bothered by what he knows of Pike's fate and condition, and from the part of Kirk, probably because he catches on to the strange mood of the Commodore. Thus, even though the phrasing might suggest that Kirk only met Pike once before and didn't really know him, we don't need to follow that suggestion: hints at a longer relationship would be erased by the terse tone of the discussion.
Timo Saloniemi