With the development of more and more plugins, especially big and popular ones like Essentials, GriefPrevention, Factions, and PermissionsEX, it's easy to forget that a server, to be special, needs to be customized and given love to. Servers like Hypixel are still great fun and have lots of players, but I do agree with you back in the spleef days where there'd be 5 people in a secret room and you'd get teleported manually. But I like to think of it this way: Hypixel gets over 50,000 players per day. Imagine how many people you'd have to pay to teleport, watch, and monitor the rules. To do it easily, they just developed plugins to automate it all.
Hypixel spent a lot of time customizing and designing their server to be unique at the time it was made, and it still is unique. The issue comes when people want to make servers like Hypixel and these big popular servers. Most of these server hosters don't understand that it takes a lot of time, dedication, and customization to actually make a good server. I used to play on a server called MCTopia, which was a server with plugins but had an experience like survival. Over time I donated, got higher ranks, and even almost became staff at one point, I knew everyone. And then one day it just crashed (not literally, figuratively). The community died out to larger, new servers with tons of plugins and customizability. Nowadays, there just isn't much respect or demand for these servers that just copy Hypixel.
Of course, there are lots of servers out there that do put in this dedication, but the issue is that they end up getting shoved to the back of server lists from all of those that just constantly say "vote vote vote for me!". This is why when I'm searching for servers, I start at the back of the list and go forward. (Of course, skipping past those hundreds of servers that are offline). Nonetheless, I think servers nowadays are still very good and fun, they've just been died down from the fact that the same plugins get used every time, and there's not much customization in the configurations of what these plugins can actually do.