Why is marginal reconstruction "more correct" than joint reconstruction in some cases?
I know this is too late, but since this is something I'm struggling with too I thought I'd post here in case others also find there way here. I don't have an answer but, here are some quotes that might help (I found them at least partially helpful).

Yang (2004): "Marginal reconstruction is more suitable when one wants the sequence at a particular node, as in the molecular restoration studies. Joint reconstruction is more suitable when one counts changes at each site."

http://aracnologia.macn.gov.ar/st/biblio/Yang%202006%20Computational%20Molecular%20Evolution.pdf

Revell (2014): 

"Joint reconstruction is finding the set of character states at all
nodes that (jointly) maximizes the likelihood."

"Marginal reconstruction is finding the state at the current
node that maximizes the likelihood integrating over all other
states at all nodes, in proportion to their probability"

http://www.phytools.org/eqg/Lecture_5.1/Revell.ancestral-state-reconstruction.pdf

Joint reconstruction is "not (necessarily) equivalent to picking the state at each node with the highest probability" (Revell 2014), but is the method of picking the tree with the overall highest MLE.