I'm not sure it's a cut-and-dried "which is worse" argument. You might have to break it down all science-style.
Countdown Pros: As you said, everyone's ignoring it for the most part.
Countdown Cons: Fifty-two weekly issues, many of which feature something apocalyptically stupid. High death count. Jimmy Olsen: Bugfucker. Forerunner.
Ultimatum Pros: Didn't affect the mainstream universe. Didn't have a lasting effect on Ultimate Spider-Man. The idea of a shellshocked band of surviving X-Men led by Jean Grey is actually an interesting starting point, if nothing else. Only five issues; killed fewer trees.
Ultimatum Cons: Probably going to be responsible for the destruction of several comic book collections, as Mom finds an issue and immediately decides the house is now a comic-free zone. Arbitrarily killed any number of potentially useful, interesting characters. Reading it makes you more stupidider.