If the quality of science in general has not increased with more people, it's getting worse per unit person.

Er, I'd just expect to see more science being done. I know of no one studying overall mechanisms of science-as-it-is-realized (little-s "science"), and thereby seriously influencing it. Further, that's not something current science is likely to worry about, unless someone can somehow point to irrefutable evidence that science is underperforming.

All of the points you list are real issues; I watch them myself, to constant frustration. I think they have common cause in the incentive structure of science. The following account has been hinted at many times over around Less Wrong, but spelling it out may make it clear how your points follow:

Researchers focus on churning out papers that can actually get accepted at some highly-rated journal or conference, because the quantity of such papers are seen as the main guarantor of being hired as a faculty, making tenure, and getting research grants. This quantity has a strong effect on scientists' individual futures and their reputations. For all but the most well-established or idealistic scientists, this pressure overrides the drive to promote general understanding, increase the world's useful knowledge, or satisfy curiosity[*].

This pressure means that scientists seek the next publication and structure their investigations to yield multiple papers, rather than telling a single coherent story from what might be several least publishable units. Thus, you should expect little synthesis - a least publishable unit is very nearly the author's research minus the current state of knowledge in a specialized subfield. Thus, as you say, existing explanations are a scattered mess.

Since these explanations are scattered and confusing, it's brutally difficult to understand the cutting edge of any particular subfield. Following publication pressure, papers are engineered to garner acceptance from peer reviewers. Those reviewers are part of the same specialized subfield as the author. Thus, if the author fails to use a widely-known concept from outside his subfield to solve a problem in his paper, the reviewers aren't likely to catch it, because it's hard to learn new ideas from other subfields. Thus, the author has no real motivation to investigate subfields outside of his own expertise, and we have a stable situation. Thus, your first and second points.

All this suggests to me that, if we want to make science better, we need to somehow twiddle its incentive structure. But changing longstanding organizational and social trends is, er, outside of my subfield of study.

[*] This demands substantiation, but I have no studies to point to. It's common knowledge, perhaps, and it's true in the research environments I've found myself in. Does it ring true for everyone else reading this, with appropriate experience of academic research?