Actually, Wandering Son was meant to be 12 episodes, but due to the earthquake/tsunami, what were going to be Episodes 10 and 11 were compiled into a single episode and 12 became 11.
Source
Fractale's adaptation actually only had 9 episodes worth of material, so scriptwriters were hired to add in 2 episodes worth on filler. Coincidence Episode 5 has someone different in charge and is a filler episode? I think not. That's what
Yoshioka Shinobu does for a living.
The length isn't the main issue. The main issue is lately noitaminA is airing shows that don't fit the demographic. This is a section that is supposed to be appealing to young adults in Japan.
What was the most popular title that aired within it? Nodame Cantabile. The final season had an 8.6% rating, which is virtually miraculous for its timeslot. It was all about adults.
After that it was The Tatami Galaxy and House of Five Leaves. 4.4% rating. Tatami sold relatively well, Five Leaves didn't. Both featured adults.
Next was Shiki and Moyashimon live action. 2.2% rating. I don't think that live action did the slot any favours. And despite the vamp/gore factor, Shiki was slow. Plus it had a fair amount of teens, which had more focus than the adults. Never heard about how Shiki sold, presume it didn't do well.
Currently you have Fractale and Wandering Son. 1.1% rating, may have dipped below 1% for a while, seem to have drifted back up to 2%. Both are shows featuring kids. That is not the demographic's target audience. noitaminA's better rating shows have had adult characters in the main roles. Aoi Hana, the other title from the same manga-ka as Wandering Son, was a good series but it effectively lead to the end of the Noise timeslot. Taking on that manga-ka's work was a risky venture to begin with. As for Fractale, its failures squarely rest on Yakaman's shoulders, which he has finally had the balls to admit.
Source Sounds like neither has sold well.
The April series for noitaminA don't quite seem targetted to the demographic either.
It's simple. Start airing shows that properly target the demographic that made noitaminA successful in the first place. And make sure you don't have halfwits like Yakaman ruining the shows they're in charge of. Get those basics right and then the timeslot can get back to where it should be.
In the end, sales are everything in this business. Quality does mean something. But it isn't a necessity to sell well. Shinbo is the king of running way behind schedule but continues to rake in the cash for Shaft. KyoAni isn't exactly striving to excel anymore but sells even when it stuffs up things like Endless Eight. J.C. Staff has shifted away from more mature shows and is focusing on moe. When a terribad show like Milky Holmes sells over 10k units, which is more than most series from last year, that says a lot about the state of the industry and the paying fans.