One of the biggest things I've noticed in a change in is similar to what Destinie touched on--there was less content and more focus on media topics like FMV screen captures, avatars, official artwork--and while that is still something some people still include in their shrines, there's less of a focus on that and more on original content. There's also not much statistical content either! For example, most characters from RPG's had a page dedicated to their stats, their weapons, armour, etc. It seems people have strayed from that a bit to focus more on in-depth topics that require more analysis than simply making tables with content on stats. That's not to say stats and lists aren't important or less valuable--simply, people have started making their shrines more about their own original content. Shrines seem to be more personal nowadays and I really enjoy that.
As far as layouts go, I've noticed less small fonts have been used and there's more a focus on bigger fonts that are easy to read, and even the inclusion of a creators own fonts that make coding look very nice. It's a good thing to stray from IMO... my glasses can only do so much. I don't like having to squint to read content. >_<