There are a LOT of anime airing during any given season, compared to western cartons from any given country. (There were about 200 that aired last season.) At the same time, the industry is small in terms of manpower, and this extends to the large companies that form production committees. (A production committee is a temporary organization formed from representatives of various large companies & represents a way for those companies to manage the production of an anime as an investment while limiting their risk: budgets are decided before any work begins, and remain static for the rest of the season, after which the production committee is dissolved.) Between these two factors, there’s less money total to go around and that pool of money, once allocated to a production, never grows. (The exception is the occasional long-running non-seasonal show — typically either an adaptation of an ongoing Shonen Jump title by Studio Perriot or a very low-budget show aimed at small children. These are very rare, and they only exist when they’re guaranteed to be cash cows regardless of quality.)

Basically all shows run for one or two consecutive cours. If sufficiently popular, they might get picked up for a sequel years later. This is very unlike the western style of television, where every show runs continuously until the ratings get so bad that it gets cancelled. This model allows for the limited nature of production companies, and it allows shows to be one-off experiments that can be discarded if they don’t pan out. It minimizes risk. At the same time, it means that subsequent seasons might not be done by the same people or even the same studio: the rights to a franchise lie in the individual companies represented in the production committees, and not in the studio, except in a handful of very exceptional cases (like Kyoani, who runs their own book publishing company specifically so that they can claim all associated IP).

The production committee model in its current form seems to have come together in the wake of Akira. However, it has its roots in funding practices that began with the first TV anime.

After the end of the second world war, the US occupying force made sure to disassemble existing media production companies — particularly animation studios — because they were producing a lot of propaganda films before & during the war & there was a fear that they would be used to resist the occupation and agitate for a return to the imperial model. (These fears weren’t unfounded: there were very active groups trying to return to the imperial model through the 70s, and while it’s taboo to discuss it, these positions are not unknown even in the Diet today. Shinichiro Abe is associated with one of these traditionalist groups, which is a little like having a US president who’s openly a neo-nazi.) This created a bit of an entertainment vacuum, which eventually was filled by broadcast TV — a lot of it re-dubbed american cartoons by the likes of Hanna Barbera (who had pretty low production quality & a lot of footage reuse). The pitch for the Astro-boy TV show was specifically that it would be cheaper to make domestically than a Jetsons license & of comparable quality — and Astro-boy was funded by a corporate sponsor in exchange for advertisements, directly. Later anime would often be funded by toy companies or candy companies, but it was a pretty direct one-to-one system. However, a change came in the late 70s and early 80s, when the economy started booming & the home video market blew up: it became profitable to create fringe shows for a small audience, never to be broadcast but instead to be sold solely through home video releases — OVAs or OAVs. This pumped a lot of money into the studios, and they started taking on increasingly complicated and experimental projects.

The biggest, most complicated one of these projects was the 1988 film adaptation of Katsuhiro Otomo’s then-ongoing manga series Akira. This project eschewed a lot of the cost-cutting measures (like drawing on twos or threes) that had basically defined anime’s style up to that point, and because of its violence, gore, sexual content, complicated story, and heady, politically-charged themes, it didn’t have the kind of broad appeal that a Ghibli film did. (I suspect that it was, at the time, more polished and technically interesting than the films Ghibli had been making thus far, but it was expensive for basically the same reasons.) A production committee was formed, consiting of almost all of the major studios, and the studios involved dropped ongoing TV and OVA projects in favor of working on this production. It was incredibly expensive. And, it bombed. (It didn’t do horribly, but it lost a lot of money simply because it was enormously expensive & couldn’t hope to recoup the cost theatrically.)

When Akira bombed, it took down more than half of the anime industry’s major studios, and shortly afterward the “japanese economic miracle” ended & a long period of economic stagnation began that continues unabated to this day. Suddenly, the studios wanted to be a lot more conservative, and they were having a hard time finding investors. The current form of the production committee became popular. (I don’t know if it began here or if this was the start of a more extreme form of an arrangement that already existed.) The individual relationships between companies and franchises that had produced things like toy companies pressuring the creators of Gundam to change the color schemes of the mobile suits went away, really experimental OVA series became rare outside of porn, and shows started having two-cour runs more often than they had 40 or 70 episode runs.

In 1995, Evangelion sort of changed the game again. Gainax had shopped the pitch around for a few years, and when they eventually got enough investors to start a production committee, they managed to snag a deal where the studio kept control of the franchise’s rights. To this day, Gainax still owns Evangelion & all the merchandising rights — something that basically never happens and was very rare at the time. Evangelion was not really expected to be successful, and production trouble caused a lot of the budget to be used up (and a lot of time to be eaten) early on, but in 1996, when it was moved to a different time slot, its popularity blew up, and it became a runaway success. Gainax made money hand over fist from merchandising and licensing rights, and this made production studios invest money into other dark, experimental shows (to which they carefully kept the rights) in the hope that any would become as popular as Evangelion. This resulted in the late-90s “late night anime boom” — a golden age for experimental shows aimed at older audiences. Few of these shows had much commercial success, although a lot of them were pretty good. The thing was, the production committees are generally not composed of anime fans themselves: these guys were trying to figure out what would sell while simultaneously seeing themselves as above the material they were selling. A lot of freedom was given to the studios because of this hands-off approach, but the production committees were pretty careful to limit their financial exposure to this risk.

The late night anime boom shifted the perceived primary audience for anime from a general one whose average age might be fifteen to a much smaller niche of independent 20–30 year old dedicated fans with disposable income. So, a lot of effort started being put into capitalizing on fan communities around particular characters (something that first showed up as a phenomenon in the 70s, and that Gainax had started out feeding). The thing about it was, because production committees only lasted as long as the production did, capitalizing on an already successful franchise with new products was hard. Instead, effort was made to ensure that particular characters would have a lunatic-fringe following, even to the detriment of the rest of the series — guaranteed sales of figurines and other expensive merchandise were very lucrative, and the idol industry showed that demand could be manufactured in a way that let small groups of fanatics hold up whole industries. The initial airing became an advertisement for the home video release — so missing or rushed footage might actually be desirable instead of a detriment, since it could be remastered or reanimated later for inclusion on home video. (Evangelion had several different home video releases with sections of re-animated content, though not as many as the US market got due to strange timing issues with ADV’s releases.)

TL;DR: all anime is funded by the same ten big japanese companies, with their budgets set by bureaucrats who don’t care, months or years before anybody starts making it, and it’s mostly intended to sell figurines and overpriced blu-rays to 30-something single man-children. There are 200 of them every 3 months, in a stagnating economy. It ends up being good mostly because the money people consider it disposable & don’t care enough to meddle.