Terrans are going for faster bio upgrades and delaying their siege tech longer. This is due in part to Terrans trying to match the double evo upgrades of the ever increasingly popular ling/infestor, but as a byproduct it reduces the effectiveness of mutas even more.
Muta balls slow down Zerg upgrades as well as delaying their hive tech. It's not uncommon to see 3/3 marines vs 1/1 or 2/1 lings with barely upgraded mutas. Take Zenio vs MMA last season in code S, there was a game where MMA was 3/2 bio vs Zenio's 1/1 lings and 1/0 mutas. And what about DRG the current king of Zerg in last seasons code S semi-finals?
Yep, he falls victim to the same thing (he lost that game). At that point you start losing mutas left and right to the most common of 8 marine medivac drops, and they'll flat out disintegrate vs a bio ball without a ton of support.
Banelings are a critical part of using mutalisks, but top tier Terran micro is disgusting. Using banelings against a T who knows how to split and focus fire tanks is incredibly inefficient, especially off creep.
It's also important to note that more macro centric builds are getting increasingly more popular for T. I could even say that an early third for Terran is fairly common. When you start trading inefficiently against a Terran who knows how to keep up in economy, it puts you in a very bad position.
At the moment I'm watching Idra's stream and every single ZvT he's been playing lately has been ling/infestor. Even Idra the king of stubbornness in his 2 base muta play is changing his style around.
I don't see any way around the problems facing mutalisk play, do you?