My major issue with ATI is their drivers. They have a history of driver compatibility issues dating way back to the early dos days, and still give similar problems today (I also hate the fact that their worse quality drivers take MORE of a system memory/cpu footprint than any other manufacturer).
Not only that, but ATI is also much quicker to drop support for older cards. Nvidia's detonator drivers are nice, they still support and optimize cards that are 5-6 years old, and all of their cards use the same set of drivers.
My other lighter issue with ATI is that as a whole they are pretty deceptive.
Until ATI corrects those issues, I personaly wont buy a single one of their cards, I have had way to many throughout the years that end up nothing more than big dissapointments.
Ill give a fair look at ATI with their new dual GPU coming in the distant future, but only if they can prove in some ways that their drivers aren't going to be flawed, and that the third party measured benchmarks show that for once they aren't stretching the truth. (which I've yet to see either from them)
EDIT: One thing I might add, so far as matrox, their drivers are decent, they have good cards for graphics professionals, but for games, their support has been pretty terrible. Quite honestly I think the 3 monitor thing in the parhelia is more of a gimmick, much like the external power source that the voodoo 6 was supposed to have. (I dunno how but they actualy fooled a lot of consumers into thinking that because it had an external power source it was more "powerful". Heh I remember arguing in #3dfx about how stupid that is, and the retards insisted that all future cards from all mfrs are going to need an outside power source, yet we have much better cards today that aren't even near needing that)