This is one aspect of the new playoff format that is flawed. If the two wild-card teams are from the two divisions, they should not cross over, especially in the West. Why should the division winners get saddled with significantly worse travel match-ups than the runners-up? If those match-ups stayed as STL/MIN and SJ/PHX it would make a heck of a lot more sense and retain the divisional flavor of the playoffs.
Alternately give the conference #1 seed the option to select which wild-card opponent they will play in the first round. That might even add a bit of fire to that series, too.