Where to begin.
I would first off like to commend you for that absolutely charming review of Apollo. I had no idea servers were open source these days; it must truly be a unique project. Oh wait.
From a very high level view, Apollo is simply a glorified Hyperion with more abstraction, more mindfucking event/thread/synchronization herpderp, and a botched attempt at scripting.
While I will agree that scripting is where we should be headed, Apollo should be looked at as no more than a step in the right direction, but by no means the final solution, or "best base out there" as you put it.
The problem with Apollo, is that it has too little emphasis on scripting. Read super_'s posts earlier in this thread; he seems to have the right idea. The server 'base' simply serves to create the model with which the scripts act on, and all of the content is only implemented in scripts not in the core.
I do like Apollo's plugin idea though, and I think that should definitely be one of the goals of future servers. For example, finding a pre-built plugin on rune-server and dropping it into your server and having it work on its own. Or, even further down the road, making some kind of package manager type thing which automatically updates plugins.
Anyway, I know this went on pretty long. The takeaway of this is that while Apollo is working towards how servers should be, it is not the final solution and definitely NOT something "everyone will be able to use" as you said.
Love,
Jim