I do like "LOST" and "Alias" as TV show models to work with.
Having a main cast to work with is great and you can have lots of rich character building, adventure, excitement, drama.
Having that large ensemble lets you focus on different situations, write complicated intricate plots, have a diverse set of interesting character interactions.
The problem with having all these great things is that it takes a set of good writers, people who respect internal logic of characters and the universe they are in.
As far as setup, having recurring cast and a large ensemble cast is what Star Trek is all about. They just don't have a consistant set of writers who understand how the Star Trek Universe works or somebody who can keep all the writers in line.
As far as what I like, I do enjoy a larger ensemble cast with a core recurring crew.
Firefly and Babylon 5 being great models to observe.
In Firefly, you always seem to have Mal and Zoe as two important core focuses, the rest of the cast seems to fluctuate as to their importance in each episode.
In Babylon 5, you generally have Sheridan, Ivanova as two important mains, the rest will fluctuate based on how important they are to an episode.
With Star Trek, the ensemble crew is a very important part. Each character getting their own focus is very important. The problem is that the writing staff can't balance who gets how much plot.
With ENT, Archer, Trip, and T'Pol get way too much screen time, the rest of the characters are 2nd tier in terms of development.
In VOY, Janeway, Seven, and the Doctor gets the most character development.
In DS9, it's alot more even with Quark getting the least development out of the principle cast. Even then Quark got more episodes focused on him than somebody like Travis who should be far more important to their respective show.
I think it's all a matter of figuring out the balance.