I can't say the Jaguar didn't have an atypical 'poor game to good game' ratio, but things related to that system aside, there seemed to be a negative tone regarding Atari in general, at least post-2001 or so when I started reading it. The ones I remember most:
A PS2 Rygar article had a comment on the Lynx version: "chunky and junky, like all games for this turd handheld. Instead, turn that Lynx into a snowboard for your cat."
An article about the G4 network had "we loved hearing how Atari founder Nolan Bushnell blew all his Pong dough" when referencing the show Icons.
There were a couple more that escape at the moment. Maybe if I end up re-reading the back issues I dug out...but last time I tried, the snarky, sarcastic "humor" in the letters section turned me off a lot more than it did back in the day (and I didn't like it then either).
They were similar though in that they felt more like cheap shots than genuine comments. Maybe EGM and Atari clashed a lot back in the days they had to deal with each other regularly? It seems like a holdover from that type of situation. If so, I have to say it's unprofessional at best. Especially considering EGM was about the only mag I trusted much, even if I didn't care too much for their "sarcastic little sh*t" approach to comedy.