Is serotonin conclusively linked to depression?
It's all about the receptors, really.  There are 7 families of serotonin receptors that perform different functions within the brain, and according to Wikipedia 14 different subtypes have been discovered. 

The article assumes that a blanket level of serotonin would be sufficient to "perk" up the brain, wherein it is much more complicated.  Serotonin serves to modulate the level of excitation or inhibition depending on the circumstances.  Most of the "effect" from today's antidepressants is related to modulating projections from the dorsal raphe in the brainstem to dopaminergic neurons in the frontal cortex, but some of the serotonergic neurons in the basal ganglia can be hyperactive in situations where there is mild psychosis.  So, depending on the etiology of the depression, suppressing those neurons local to that portion of the anatomy can actually be helpful.

So, it's less to do with the transmitter that is being discussed, and everything to do with which subtypes of receptors are being agonized or antagonized.  While we have learned a tremendous amount about the relationships between neurotransmitters at different nuclei, we still have a lifetime or more of research to go.