I think there's a difference between the dry definition of a port and the thing that people complain about.
The term "a port of a game" means a game was developed for one set of platforms, and it was later released for other platforms. Technically, a game released for multiple platforms from the get-go - such as Crysis 2 you have mentioned - shouldn't be called a port.
But that's not what people complain about. A game can be a port from its version on another platform, and still be a great game which was carefully ported. What people really complain about are games that exhibit elements not appropriate for the platform they are running on; unfortunately, this is a common occurrence with ports, hence the connection.
The problem isn't really exclusive to ports - a port may be a good port (modified to fit the new platform perfectly), while a non-ported game released on many platforms may simply work better on one platform vs another. The truth is, though, that many game today are designed with consoles in mind, and unfortunately their PC version (whether a port or a simultaneously-released version) is inferior because they are not properly adapted.
Common examples of things not properly adapted are UI elements - e.g. where mouse navigation is lacking while keyboard navigation is fine; aiming - where in consoles FPS often have auto-aiming mechanisms that should not appear on the PC; driving - where the accurate gamepad control does not have a parallel in a PC keyboard; etc. One of the biggest ones is something a little less obvious, and that's performance - a poor "port" might have poor performance on the platforms it was not originally designed to work with.
EDIT I've recently found this nice piece listing problems or missing features that plague PC releases of console-oriented games nowadays. Although it specifically bashes some select titles, it does mention problems that I've seen in many recent games, and I thought it's worthy to include the link here.