I'm not claiming Madrid are up there with those teams so I have no real problems with your conclusion, but rather with how you reached it. You havent really taken into account the competition and strength of the leagues that those sides faced. Bayern in 12/13 won their league by 25 points (that is not exactly being pushed to the limit like Madrid are being now) and drew both games with Dortmund 1-1 (so that goes against what you said about them doing consistently well against the top sides, in the league at least which is what I assume you are referring to as I am sure your post is a response to yesterdays result). Dortmund were obviously strong as evidenced by them reaching the final but they were not equipped to put in a strong challenge for the league as well as in Europe.
As for Barcelona under Pep. What top sides did they have to overcome domestically? I will give you Madrid under Mourinho but that was by 10/11. Madrid in 08/09 were not exactly anything special. Going out in the Copa in the 4th round to a third division side, finishing 2nd in the group to an average Juventus and losing both home and away to them. Getting smashed 5-0 on aggregate by Liverpool and losing both home and away to them. Getting annihilated 6-2 at home to Barcelona as well as having lost to them at the Nou camp as well. They also lost 3-0 vs Valencia away as well. And Madrid were the only other team in the league at the time who were seen as strong other than Barcelona. Not exactly what I would call tough competition.
The following season Madrid improved but not really by much (nowhere near as much as they should have after the money they spent). Once again they went out in the 4th round of the cup losing 4-0 (4-1 on aggregate) to Alcorcon (a Segunda Division B team), they actually managed to finish top of their group in the CL this time albeit were still unable to beat a poor Milan side and even lost to them at home in one of the games (and this really was a poor Milan side, which lost 7-2 on aggregate to United in the last 16 and finished third in Seria A). Madrid then went out in the last 16 once again, being unable to beat Lyon once over two legs (tbf this Lyon team was good, but not great. They lost 4-0 on aggregate to Bayern when they met. A top team should not have lost to Lyon). In the league once again they were unable to beat Barca or even score against them.
Quite simply they were not one of the top sides in 09/10 despite the money spent. Barca, Milan, Roma, Inter, Bayern, United, Chelsea, Arsenal and Lyon were all better than them that year (maybe even some others). And just like the previous season they were the only other side in Spain that were considered strong. Tbf they did push Barcelona in the league, but going by the results that I posted in earlier in this post, I think that just reflects badly on La Liga back then rather than the strength of Madrid or at best shows that they had the potential to be a top team, but were not one yet. And even if you think Madrid were a good side that season, they were not as strong as Atletico are this season or last season, or as strong as Barcelona are this season or last season. And despite the ease at which Barcelona won games in the league during those years in addition to the ease in which they beat Madrid, their away record in the CL was not the greatest, especially in the knockouts (which doesn't reflect well on the rest of La Liga).
Like I said, 10/11 is fair enough as Mourinho made Madrid into a top team and one of the very best again. But simply using results against the other top teams like you were is very faulty and lacks context. It does not take into account the quality and competitiveness of the leagues these respective sides were in. La Liga this season and last year is stronger than it was back when Barcelona were dominating. I think it would be fair to say that Peps Barcelona would not have always gotten favourable results against this Atletico side either (we all saw what happened when his side faced Inter and also when they faced Chelsea in 08/09 and their less than stellar midfield in 11/12. Heck even Atletico back then were good for a result against them despite not being as good as they are now). United from 06 to 09 did not always get good results in the big games in the league (the only big game they won in 08/09 was vs Chelsea at home) and that was not because they were not a good side. They were a very good side and a very dominant one I might add too despite these results which goes against your logic. Its just that they were playing in a very competitive league which was very strong at the top. Which is what La Liga is now.