This progression has been occurring since about 2001 or 2002. Also, when the Internet burst onto the scene. Whether or not that is a coincidence is up for debate. But this pattern has been trending since that time. There has been an increase in the depth of quality.
However, if you go back and study this on a NCAA Division III level you will notice, with only occasional blips on the radar, that it's the SAME 60 schools (out of now 500) that participate at cross country and track & field nationals. Why is that? Same as it has always been: recruiting and development.
Let's take recruiting. It boils down to each coach finding the school's niche and then his/her ability of the to sell that niche. It's rather easy when a school falls into one of three categories: inexpensive (also usually large student bodies), academic prestige, or religious affiliation. The other is tradition. This may or may not tie in with the above three categories.
For example, Haverford is prestige + tradition. Calvin is religious affliation + tradition. North Central is just tradition (so-so academics with relatively high tuition). In other words, it is most impressive what North Central (i.e., Al) accomplishes year-in and year-out. So what you have is of the top 25 names in the 5k/10k are few exceptions to this rule. The coaches from Edgewood, Juniata, Rowan, and Franciscan (maybe getting something started by selling religious affiliation) should be complemented as they are the true anomolies and don't really fit any of above categories for inexpensive or prestigious schools. Actually, it's impressive what any of these school accomplish in Division III. It's pretty well known within the industry (at least coaches, if not administrators) that many of the best recruiters and developers of talent are in Division III.
Now take development. There was a time 15 years ago that a 10:00-kid could develop into a 31:05 college 10k runner. By the way, a 31:05 = 9:10 for 3200m. That's "development". This guy would not only make nationals, but probably be an "All-American" back in the mid-90's. Fast forward 15 years and now a 9:40-kid (typical D3 recruit...used to be a D1 walk on) is developing into a 14:19/30:10 college 5k/10k runner.
You might not see it much on D1 level, but that's because, generally speaking, many of the best "developers of talent" are at these 60 D3 schools. Just spend some time with Tom Donnelly, Al Carius, Don Nichter, Jeff Stiles, Mike Woods, Brian Diemer and you know you've met a great coach in a great situation. It's a formula for success that repeats itself time after time. Again, the fascinating situations are those kids running fast from schools outside the traditional 10% that always run well. Who are the new kids on the block so to speak? Who is recruiting and developing from a position of weakness vs. a position of strength? Recruiting practices are getting better/easier in D3 with increased communication (plus, there are less men's programs and less $ for men in D1). But any way you slice it the best development, from many of the best coaches/teachers, continues to occur in D3.
I personally believe that this occurrence is not an anomaly, but D3 is finally nearing a glass ceiling. The trend started a decade ago and D3 has arrived at its destination. From this point forward, D3 coaches will need to recruit 4:27/9:42 or better kids, then develop them into 4:05/8:53 college runners capable of running 14:19/30:10 in order to be a "D3 All-American". Well done D3! Enjoy "Baby Nationals"! It's the best kept secret in all of cross country and track & field. There's nothing greater than Division III athletics.