Dortmund are better than Atletico and Arsenal fared fine vs them...
Dortmund aren't really that strong this season, hate to say it. 3rd in Bundesliga behind the Leverkusen side that just went down 9-0 to United on aggregate. And yes I know, saying that one point alone isn't enough to discredit Dortmund as a side but it's easy to see that they aren't as capable of taking down the elites as they were last season.
Atletico are capable of beating Arsenal, it's a pretty close contest though. And Semi, you pointed out that Arsenal would have the stronger midfield game, and you were correct, but that isn't where it would actually be won. Atletico made Barcelona's best midfield seem sparkless despite them being in control, with the added factor of Messi. That makes me fairly sure that even if Arsenal control the midfield, they won't be able to get past them and create attacks without immense difficulty.
As for the La liga criticism, it's well warranted but over the top. Athletic this season are also quite impressive and gaining form, Villareal even more so; neither are title contenders, but easily capable of providing a challenge to their EPL counterparts. It'll be a while before La liga is on the level of BPL in terms of competitiveness, but that's really down to the style of the league being much more tactical rather than unpredictable, plus the midtable sides are only just starting to grow.