Code Geass's first season. Sunrise was wary of trusting a full series to director / co-creator Goro Taniguchi, thanks to his reputation for perfectionism and his other quirks, so he was only handed 25 episodes to begin with. The staff often had to piggyback off of other parts of the studio that were working at the same time (for example, the Geass staff didn't even have their own photocopier) and the writers were only three or four episodes ahead of the broadcast, about half the "buffer" that most series have. When the series became a runaway success, things went much better, but fans tend to blame the series' being split in half for the perceived drop in quality in the second half.
The Dream Machine, the final movie of the lateSatoshi Kon, has experienced its share of trouble, having gone from production into Development Hell, back into production only to fall back into development hell. First Kon's death from pancreatic cancer put the film on hold to determine the next course of action. Kon's widow and Studio Madhouse's Masao Maruyama said they would finish the film and production resumed. However, at Otakon 2011, Maruyama reported the movie has been put on hold due to financial difficulties. Maruyama is still determined to finish the film eventually, with about 600 shots out of 1500 had been animated at that point.
The Fruits Basket anime was full of this, as Natsuki Takaya not only was more involved than other authors in it, but she had huge Creative Differences with the director Akitarou Daichi. This is cited as the reason why there is no second season, despite the series' popularity and its open ending.
Zeta Gundam, which suffered fewer financial hardships than the original, but both the TV series and its Compilation Movies rather infamously suffered complications as a result of the romantic blunders of various men involved in production with at least three voice actresses. Most infamous of which was the legendary feud between the Prima Donna Director and scriptwriter Yoshiyuki Tomino and equally self-important mecha designer Mamoru Nagano. It became doubly notorious because not only both men were feuding over the Beltorchika Irma's voice actress Maria Kawamuranote Nagano won and they still seem to be Happily Married., but over Creative Differences as well.note Nagano routinely hated Tomino's style and the direction where he was taking the show, up to the point that The Five Star Stories basically started as his Start My Own towards their other collaboration, Heavy Metal L Gaim.
Mobile Suit Gundam SEED Destiny also suffered this, partly because of head writer Chiaki Morosawa's battle with cancer during production, which resulted in her turning in scripts in late, which necessitated the numerous clip shows throughout the series. Secondly, although Shinn was supposed to the main character of the series, Kira was thrust back into the spotlight from episode 39 onwards, because of his popularity with the Japanese audience. Finally, there was director Mitsuo Fukuda being demanding on the voice actors on the way how they're supposed to to be portrayed (specifically, Naomi Shindo [the voice of Cagalli] and Maaya Sakamoto [the voice of Lunamaria]). This was confirmed by Rie Tanaka (the voice of Lacus and Meer) at her 2008 New York Anime Festival appearance, as well as Kenichi Suzumura (the voice of Shinn) in one of his Twitter posts.
Hols: Prince of the Sun was being made when Toei was restructuring itself to focus more on cheaper productions over lavish animations, and when its animators were starting to unionise. By coincidence, most of the aspiring, "troublesome" pro-union animators were assigned to work at the studio focusing on lavish animations, one of which was Hols. Originally intended to be a two-hour epic, the film was cut down to just 80 minutes as it exceeded its then-standard eight-month production period. When the film was finished, Toei did very little advertising and gave it a theatrical run of only ten days. At the end of it all, Isao Takahata was demoted, told he would never direct again, and Hols became an influential classic widely hailed as one of the best anime ever created.
Hyouge Mono had a few cases of some behind the scenes drama. It started with the band member of cro-magnon which co-composed the music and wrote the theme song getting arrested on a drug charge suspicion then the original author and the editorial staff walking off the project and asking for a credit change from Original Creator to Original Concept.
Lost Universe is a notorious case. The show's budget was already low, but a studio fire resulted in lots of work from the first few episodes destroyed. They had to be reanimated on an even lower budget by a South Korean studio while the rest of the show resumed production. This all occurring during a recession. One episode looked so bad on TV, that it had to be almost entirely re-animated for home video and re-runs.
For a long time, Mahou Sensei Negima! looked like a happy subversion. Ken Akamatsu wanted to do a shounen-action series from the start, but his producers wanted a harem show like his extremely popular Love Hina series. Akamatsu faked a harem series, using the first two volumes to lay down characterization, then slowly segue into the fighter series he wanted from the start. This resulted in an extremely intelligent and popular series known for its Amazon Brigade and ridiculously badass ten-year old protagonist. However, some three hundred chapters later, the executives tried to take the rights to the series away from him. He responded by ending the series abruptly, with a carefully crafted final chapter that managed use the "Where Are They Now?" Epilogue to make sure no one else could use his series. It remains to be seen if there will be any more releases filling in the unanswered questions.
Neon Genesis Evangelion. Creator Breakdown and severe depression on behalf of Hideaki Anno, Gainax's shifty accounting practices ending in their CEO being arrested for tax fraud, sponsors pulling out in droves once the show dove off the deep end... Yeah, it's amazing that they even managed to finish that show, even with all the budget-saving Limited Animation at the end. Do we have another candidate for the Apocalypse Now of anime?
Super Dimension Fortress Macross had shades of this trope. Originally envisioned for 48 episodes when the show was first greenlit, one of the financial backers went out of business, forcing a cut to 23 episodes when a new backer was found but did not have the money to fund the original 48. But the show was a hit upon premiere. And so, to bump the episode count up, they brought in legendary production company Tatsunoko. They foisted upon Studio Nue a host of questionable farm studios who brought in Off Model work, and even at one point managed to get a nearly-completed episode left on a train, nearly forcing a complete redo of the entire episode. And then, the fact that Macross was a hit and the interesting financial situation between Big West and Tatsunoko caused the production to be troubled long after the last episode went off the air. Even the title was due to Executive Meddling, as one of the producers, an admirer of Shakespeare, wanted the show to be called Macbeth, and had to be negotiated down to Macross as a compromise.
American fans were thrilled when Funimation got a hold of the 3rd Tenchi Muyo! OVA series. However, Funimation screwed up the contract and only got the rights for the first three episodes. It took a year to renegotiate for the other four episodes and get them out, barely averting a case of The Other Darrin when voice actor Bob Papenbrookpassed away soon after the release of the series.
This trope already occured when they got back the entire voice cast... except Ryoko, arguably the most popular character in the show. While the details of what happened are kept private, her original voice actress, Petrea Burchard, simple said "we just couldn't work it out." This change remains one of the more controversial aspects of the OVA.
The Vision of Escaflowne television series went through several years of Development Hell, in which time the attendant manga series based on pre-production materials was being published, and by the time the series itself made it to air they had to abruptly cut down the plot from their planned 39 episodes to 26, resulting in a very rushed ending that lacked much closure and left several plot threads hanging.