The Binaltech and Alternators line were notorious for Executive Meddling in the form of the car companies whose car models they tried acquiring the rights to make figures out of, as a good deal of these demanded that the guns that came with the figures were either modified or completely removed, or just flat out refused to hand over the rights period, in order to prevent them from being associated with "war toys". That doesn't mean that there wasn't plenty of in-company Meddling, though; in one memorable instance, Takara demanded that a new Dodge Ram figure Hasbro was making be turned into Optimus Prime, so they could sell it more readily in Japan. Since Takara was needed to front part of the cost, Hasbro agreed... only for Takara to market the figure as Masterforce's Ginrai, not Optimus. Then the figure was delayed for a number of months, prompting rumors that it had been canceled. The rumors turned out to be partially true; the Ginrai figure was canceled, but it got a release as Optimus Prime in the Binaltech line's Kiss Play sub-line, as well as a black repaint release as Black Convoy. The figure was ultimately released in the main BT line, as Optimus like planned, as the final figure.
The Transformers Animated cartoon premiered on December 26th, 2007, with regular episodes starting in January. However, Hasbro executives decided against releasing the related toyline on the same date and instead released them in June, since the toyline of the 2007 film was still selling strong. ThisShortpacked!! strip (and this one too) comments on the delay.
The process repeated itself with Transformers Prime, which began in earnest in February of 2011 and didn't get a toyline until December... and only in some parts of the globe. But in all fairness, as a lot of countries received the show much later than the English-speaking ones, this great release date slip didn't have as much of an impact on them. The canceling of the more popular First Edition toys in most markets, however, did.
The reason why Transformers Generations figs and other popular lines aimed both at kids an collectors don't see a release outside of a select few lucky countries is that allegedly distributors are convinced that the simplified, gimmicky figures sell better. At least, they certainly are more suitable for little kids than the more complex "main line" toys.
The original 1960s metal Thunderbirds toys had a blue Thunderbird 2 after the original production run — to Gerry Anderson's dismay — because the marketing drones said that "children don't buy green toys". A small touch of irony comes from Derek Meddings' original concept sketch for "Rescue 2" (as TB2 was then called) specifying that the craft was blue.
The shift from gear-based mechanisms to gimmick-free but highly poseable toys and the abundance of launching weapons are also examples, but they had solid reasons behind them: kids like toys that you can quickly slap together and shoot stuff with, instead of messing around with complex gear mechanisms and other features — some of which only detracted from the toys' better aspects anyway. Still, fans found reasons to complain.
In the Mistika figure line, the three sets out of the six that represented three of the initial BIONICLE line's main characters were vastly different from their original forms: the muscle-bound hunchback Onua became a tall and lean fighter whose mask wouldn't look out of place on a villain; Gali, the female of the group received a hunched posture, long bunny-ears and a (as fans call it) "waffle" eye; while the leader of the group, Tahu... fared relatively well, though his lost his classic fire sword in exchange for a spinning shield, and had something of a samurai theme going on with his mask. In-story explanations made it clear that these were just temporary forms.
The BIONICLE Stars line was an example of the creators managing to come to an agreement with the execs — LEGO originally wanted to end Bionicle abruptly and without giving the story a satisfying end. Instead, they agreed to give the toy-line another half year and allow the writer to tie up at least some of the main plot-lines. Even so, Stars was hit by some meddling — instead of the normal-sized "Canister" sets, they were only "Impulse-sized" small sets with limited articulation and out of scale with the rest of the series.
2005 was this in its entirety. Originally, the Metru Nui Whole Episode Flashback saga would have lasted for only one year, but designing the setting cost so much that LEGO pushed it further, even though the story had already been wrapped up in '04.
The notion that "boys find girl toys icky" was one of the reasons why they banned romance in much of the story, but some speculate it's also why many of the female characters were made to look masculine and often ugly (Hahli Inika even receiving mustache and beard ornaments). Roodaka was just about the only toy whose gender could be identified by looking at it, though allegedly her design has caused such a controversy among some groups that the designers had to make all subsequent female figures more generic, if not outright manly looking.
In the 2015 reboot, Lewa was originally supposed to possess the element of Air, like in the original line; but due to LEGO having received many questions as to why green toys represented air, they changed his element to Jungle.
My Little Pony gets some of this. The manufactures have to make things that the stores are willing to stock, and the stores want the girl toys to look as girly as possible, thus sometimes limiting the pony designs to little more than a Tastes Like Diabetes checklist:
The reason why the toys for Princess Celestia were initially pink while the character on the cartoon series is white is because a pink toy would appeal more to young girls; apparently a whiteWinged Unicorn princess with rainbow hair wasn't girly enough. This is presumably why the season 2 finale introduced Princess Cadence as a new pink winged unicorn character, since from that point on the Celestia toys were accurately white (with some hints of pink on the wings of some releases).
And, on that note, this is why Celestia's a princess and not a queen. Lauren Faust originally wanted Celestia to be a queen but Hasbro felt that a princess would be more appealing to the young girl audience. That said, if it's a country where two people share leadership duties equally they're not queens anyway. (Some have said that it was actually because they thought Disney had "tainted" the term "Queen" to represent someone evil.)
Celestia's sister Luna seems to also get some of this, since most of the Hasbro-made toys of her are purple instead of the blue of her show design, and she sometimes gets pink streaks in her mane that don't resemble her animated counterpart's blue mane at all. Licensed Lunas like the Build-a-Bear plush and the Funko vinyl figures made for adult fans are more on-model.
Some of the less girly-looking toys seem to only get through due to being sold in sets with girly ones (usually rereleases of common ponies) added in as peace offerings to the toy stores. Collectors sometimes complain of having small armies of Pinkie Pie as a result, since she's the most common thanks to being very pink.
Applejack is the least feminine-looking member of the main characters of My Little Pony: Friendship Is Magicnote being orange with yellow hair, instead of pink, purple or rainbow like the others and so she tends to get much more sporadic releases than the others. She was blatantly left out of a large set from the Ponymania line which contained every other member of the Mane 6, plus Celestia to take Applejack's place, as well as a mid-2015 McDonald's toy line which instead featured the much more feminine Coco/Miss Pommel (who, while popular and a recurring character, doesn't appear nearly frequently enough to justify the decision).
The Bratz line of dolls was eventually reduced to either Cloe & Yasmin (Or Closmin) or clones of Cloe and Yasmin with the occasional different girl after every 7-9 lines because Cloe and Yasmin were the best selling dolls.
The Avatar: The Last Airbender action figure line never feature a single female character, not even the ones on the main cast. Even Jet, a male character who appeared in about five episodes before dying, got an action figure. Apparently it was based on the idea that female action figures wouldn't sell. The Legend of Korra, a Sequel Series with a female lead, doesn't have a toyline at all.
Over in Executive Meddling/Anime, it's mentioned that the Dub Name Change of Gundam units such as the God Gundam and Devil Gundam was mandated by Sunrise/Bandai. The reason for it was because of the toys. You see, when the initial sets of Mobile Suit Gundam Wing figurines came out, they had left the names alone. When Walmart stores got shipments of the figures, they were appalled at one of the figures - Gundam Deathscythe Hell. Being a family-friendly store, Walmart ordered every last Deathscythe Hell figure returned to Bandai. Bandai fixed this by renaming it "Deathscythe H".
Ironic enough, the ''Endless Waltz" kits sold in Japan went the opposite way for said Gundam: It's named "D-Hell" on the packaging.
Monster High was rebooted in 2016 to highly polarized opinions. The motivation was to expand the target audience to younger kids, which caused fans of the (slightly) edgier tone to be upset, and many complained that the edge was gone due to the softer faces, despite the increased detail on older characters. While the tone shift can easily be explained, the cost-cutting measures such as the absence of doll stands and cheaper boxes seem to have been tacked on to the reboot to excuse the changes. (Interestingly, sister franchise Ever After High had similar cost-cuts and updated faces, but not a reboot.)