well, two problems. each side girl was given an arc in which they are allowed to grab the attention. yes, nagisa is there floating around, but there was equal attention, and importantly, this attention does not generate the reflexive "how does this affect nagisa" drama that is typical of romance animu. (compare with true tears, for example. every hiromi or noe good moment is a tug against the other side. harem animu relations are most notable for this stand along independence, which clannad shared in large chunks)
the other problem is lack of sustained development until the arc itself. it may seem sustained if you are rooting for nagisa, however, there are scatterings of development for other characters as well. i even recognized that nagisa's moments were more significant as far as her being the chosen girl is concerned, but the lack of emotional and romantic depth is wanting there. i do not recall any impact scenes with nagisa, showing her character, not merely the all too obvious fact that they liked each other. the simple gestures like food gifts are not enough, since everyone else does it as well. nagisa must do significant things that stand above the other girls, otherwise the choice will appear arbitrary.