Spoilers(Just in case)
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The show is genius, fast paced in both terms of plot and film style, but not lacking in emotional development. TV is a great medium for dynamitic story lines and change, but all too often shows are static, and unwilling to adapt or alter certain conventions,(see x-files, and Star Trek).
Alias is definetely not one of those shows.
The characters are complex, their motivations are often conflicting.
It made sense to destroy the Alliance, and the show did it fast, like the writters felt the Alliance dismantling was Q.E.D, and moved on to more intresting avenues. Sometimes you cant even blink during an episode for fear of missing something,(I missed 10 minutes of an episode last year and spent the off season part thinking Will Tippen was dead).
Rather than leaving us in the Mulder/Scully romantic dead zone, they advanced the plot and the situation.
And How much does someone want to bet the new Maxine, is the black woman from K directorate that Sidney would go head to head with.