The Ninth Circuit addresses that argument in some detail: it points out that just because a foreign suit is meritorious doesn't mean it isn't an attempt to do an end run round the US court. The US action was filed first, and Motorola's attempt to seek an injunction in a more favorable jurisdiction seems like a transparent attempt to apply pressure in the first-filed action.
The US courts take international comity seriously; one of the three factors the court considered was whether the injunction was an intolerable affront to US-German relations. But here the US action, in addition to being first, would also plainly resolve the German action, since what the US court is deciding is whether Motorola is obligated to grant a worldwide license to Microsoft. If it does, then Microsoft gets a license and Motorola isn't allowed to assert its patents against Microsoft *anywhere*.