When I talk about how a game is "structured differently", what I mean is that the proportion of its different elements is different from what some people expected.
For example, take Wasteland 2. The game's opening areas are let's say, 30% less "talky" than what some people were expecting from a Fallout-like game. They have 20% more combat than what they expected, and 30% more containers to unlock than what they expected. All the classic elements are there, but to some people - the most nostalgic people, those most hardcore fans of the old games - the proportions feel "wrong". And to some of them, that's a deal-breaker, a game ruiner.
If that sounds petty and petulant to you, then yeah, it kind of is. Most people aren't that fixated on how the old games felt. They just want to have similar mechanics and overall feels. But them's the digs.