No, because they both start with the phrase "All friendly characters with the Avengers team ability have the following team ability instead of the Avengers team ability:" replacing the current TA. Once you pick Thunderbolts, the figure is a Thunderbolt and can't use Alpha Flight (and vice versa). Theretically, I guess you could have both cards on your Avengers during the team building phase (since everyone is still an Avenger at that point), then when game begins decide which card you'd rather use. However, since you can just choose to use the Ultimate X-men TA with Thunderbolts, there is really not much point in using the Alpha Flight card.

Except for thematic purposes, of course.

and points, if I'm not mistaken...