I can't be definitive on this, but here are some aspects I've observed.
Independent Affiliates of the UUA have (or had?) the right to sponsor seminars at General Assembly, and set up booths in the exhibit hall (but they still had to pay for them, at a reduced rate). There was some concern at GA that there are only so many rooms and time slots for seminars, and that resource should be used for things that bring us together, rather than groups at the fringe (or frontier, depending on your point of view) that have their own exclusive agenda. PeaceBang's note later in the blog detailing that perhaps a large church threatened to leave the UUA if UUPA was officially recognized as an IA sounds credible.
A similar conservative sentiment was expressed at the GA where CUUPS was recognized, many years ago. In a speech, a former president of the UUA said something like, "the media already looks at UUism as a fringe movement, and bringing witches and warlocks into the denomination will marginalize us completely." Luckily, the GA didn't see it that way, and paganism was accepted as one of the Sources we draw from.
Another issue, besides having an abundance of groups pulling in different directions that a core message is diluted, is money. Affilliate organizations have their own fundraising, their own magazines, their own demands upon the volunteer labor pool. The UUA is in competition for these resources, and in an age when we're facing battles with other corporate structures with many more resources, it wants to centralize and channel resources where they think it will do the most good.
However, most individual UU churches see the UUA in the same light! They don't want their congregations to do so much for the denomination that they have nothing left for their local congregation. Most UUs have little awareness of the office in Boston, or of GA. It's a very loose Association as organizations go...not at all like other denominations where they own the buildings and assign the priests.
There have also been, through UUA history, conflicts between the board in Boston and its youth organizations...there's probably a thread on this forum's archives that is about the YRUU (Young Religious UUs) and its funding from the Board being changed. I imagine the UUA board is trying to set a policy that will be consistent and avoid controversy. It's a bit like closing the school cafeteria to avoid food fights.
