I think ENT's most basic problem was simply this:
They'd been doing it too long.
I mean, by late 2001, when ENT premiered, Rick Berman had been on since TNG Season One in 1987 -- fourteen years
. Branna Braga had been on since, IIRC, TNG Season Season Four -- eleven years. On top of this, both were under intense pressure from UPN executives to keep ENT according to TNG-style formula, to keep from experimenting creatively and innovating, to keep Star Trek
from evolving along with the rest of the television medium (which was, after all, just starting to enter the Modern Golden Age of Television, with programs like The Sopranos
, The West Wing
, and Six Feet Under
all being contemporaries of ENT).
So when you combine these things, you have a recipe for creative stagnation. It's really no wonder that it took Manny Coto, with his willingness to innovate a new storytelling style (successive three-episode arcs), his willingness to embrace Star Trek
's political heritage (e.g., the Vulcans planning to invade Andoria on false allegations of their developing a Xindi WMD as an obvious allegory for Bush invading Iraq), his fresh take on how to link ENT with TOS, and his over-all sense of fun
, to make ENT such an enjoyable show in the fourth season.