That sounds like a book worth of answers. I'd look at Peter Warren's blog (Saruyama Bonsai) as he has attended the show. My teacher and I had a number of conversations about the Kokofu-ten and how things have changed over the years. Quality levels on trees have gone down in some respects but it's not like the show is by any means non-impressive.
One thing that has changed for sure is stand and kusamono selection. Stand sizes have decreased for some styles of bonsai as have kusamono. While we think of bonsai on display nowadays as "Traditional", it is fact Contemporary overall. Take a gander at Kokofu 50 or so and see how things have changed. I personally like to follow what kusamono (shitakusa) are used at exhibitions as these display elements don't often make it into the photos of major exhibitions. Many of the old Japanese magazines do track them from year to year though. I've seen more Chojubai, willow, and cotoneaster used in concert with perennials and moss lately (last 3 years).
Again, look at what Peter Warren has to say about the containers used. From my perspective, trees exhibited at the National Exhibition in Ueno are put into high quality containers as a matter of fact. Some of the choices don't really work for me. Kichou (Precious Bonsai) are pretty much automatically accepted into the Kokofu-ten unless they are just horrible looking and sometimes their containers are not as spectacular; this can be for health reasons.
It's blatantly obvious that attention to detail for styling of branches has increased (from say the early 80's to now) and some may argue past the point of natural into something more synthetic (and I use those sweeping terms very loosely). No hate mail please
Selective pressure for only the highest quality bonsai has given way to filling up the show from what I hear; an issue present in American shows and elsewhere.
I have one beef with the National show and that is the restrictive nature of what sizes and species of plants are allowed into the show. An 8" maple may get in but a 9" one of the same quality in every way won't as it will throw of the vibe of the overall show. These measures were put in place to make the show "flow" better, but I feel it limits what can be seen there. It's a difficult issue to overcome though with so much bureaucracy. My beef lies with the effect this has on what bonsai are created or more so refined to match the guidelines for the big shows as these trees have greater monetary value. Saying "this tree is the right size / style for the Kokofu" is a common sales point....