Atletico are a tougher opponent now, you can even see it in the way they continue to stay close to Barcelona in La Liga, while Real have problems with their defense, which is not always able to play well. And Atletico's attack looks much better now, they have great forwards, so maybe Real remains the favorite, but not by a very large margin. Real's attack is also very good, and Atletico will have to rely on their defense.
Atletico Madrid is a tough opponent for any big club in Champions League but by understanding Real Madrid very well, they are one of most unwanted opponents with Real Madrid. Similarly Bayern Munich did not want to play with Bayer Leverkusen in Champions League too but destiny attracts them playing against each other.
I think both pairs are hardly predictable as Bayer Leverkusen and Atletico Madrid even can be considered as weaker but not too considerable, and they are able to play outstanding matches to beat stronger opponents like Real Madrid and Bayern Munich. Personally, Atletico Madrid have better chance to win than Bayer Leverkusen.