I guess this is a fairly minor gripe, considering it doesn't ultimately affect the gameplay in any major way. I read through the 2006 wishlist (for the nth time) and found that it was only lightly touched on so I thought that it was worth posting, even if it is too late.
I can't remember whether this has been a recurring problem (although it seems unusually prevelent in 2005), but the user interface is seriously lacking in terms of standard PC interactivity. There are no keyboard shortcuts (you'd think atleast ENTER and ESCAPE would be universal enough), no mouse wheel scrolling, and no navigation by arrow keys. Literally every interaction with the UI, besides instances of naming savegames or created players, involves using the mouse (which only utilises left click). This is particularly bothersome when using the email feature which, having no central inbox or file tree view, is an excercise in tedium to use.
I've been a PC user for over a decade now (and an NBA Live user for the same amount of time for that matter), and to be placed in a game that is UI heavy (a lot of time spent interacting with menus and the like in dynasty mode) it is really starting to grate on my nerves (probably more than it should) that the keyboard and mousewheel literally have no control over navigation.