Animated features originate under two sets of circumstances today. One set of features comes from ongoing studios such as Pixar, DreamWorks, and Blue Sky. They are characterized by large staffs and high overhead, which result in films with high budgets and the need for massive success at the box office. Budgets are routinely $75 million and up.
The danger of this model comes from a box office failure. Should a film flop, the loss is enormous. Pixar and Blue Sky are owned by larger corporate entities (Disney and Fox respectively), while DreamWorks is independent. While Pixar and Blue Sky might be better positioned to survive failures, Disney (which shut down drawn animation) and Fox (which closed down Don Bluth's Arizona studio) have both proved that corporate parents are not always forgiving.
The benefits of the Pixar-type model is continuity. Mistakes and breakthroughs that occur on a project increase the corporate knowledge base, improving the quality of each successive film.
The other type of animated feature comes from producers who assemble teams or find subcontractors for single films. These films are lower budget, perhaps as low as $15 million, so they don't need to gross as much at the box office in order to make a profit. Generally, when a film of this type is complete, the crew is laid off or the subcontracting studio left to fend for itself. The next time the producer gets a film underway, a new crew is assembled or a new subcontractor is found. Even if the same subcontractor is hired, the odds are that their crew has turned over unless the subcontractor was lucky enough to find a constant flow of work in the interim.
These producers, frequently struggling to find financing, often put their productions in whatever location offers the best financial incentives, such as direct investment or tax breaks. John Williams produced three features, Valiant, Everyone's Hero and Space Chimps, in three different cities with three entirely different crews.
These two approaches result in an increasing gap in production values (and often in scripts as well). While Pixar, DreamWorks and Blue Sky raise the bar with every new production, the one-off features are figuring out the basics for every film. While they are busy re-inventing the wheel, the larger studios are inventing teleportation devices.
I think that there's an alternative model that falls between the two. The strength of the larger studios is skill and knowledge continuity and the strength of the independent producers is low overhead. A combination of the two would raise costs somewhat, but would also allow a producer to make increasingly better films.
A producer could assemble a small team of fewer than 20 people who would be permanent employees. These people would be the equivalent of department heads. They would need to be experienced and flexible. For each project, these people would do prototyping, figuring out how to solve production problems, building a pipeline and setting the style for the film. They would take sample shots to completion, so that every stage of the production could be tested on a small scale. Once they have workable solutions, the production could then seek out subcontracting studios.
The department heads would have to relocate to wherever the subcontractors were. Their job would be to work directly with the crew, educating them as to how the production should be accomplished. They should also work with the crew individually, learning everyone's strengths and weaknesses. Too often with subcontractors, studios only have contact with supervisors and so are ignorant of the talents of the crew. Casting talent is one of the most important and powerful tools a production has to put quality work on the screen.
Because the department heads will have first-hand knowledge as to how the film should be produced, subcontractors should be able to work efficiently. Inevitably, new problems will arise during production, but because the department heads are physically present, they can contribute to the solutions and take the knowledge back with them to the parent company once the production is complete.
The producer has to find the money to keep the core team together. Without it, the result is the John Williams model of starting over with every film. Ideally, budgets can be kept low enough with this system to allow for sufficient profits to make this possible. Of course, this assumes that a producer is interested in a better product rather than a quick profit.