Frankly, the impression I get is that they were chugging along producing the episode arcs, then all of sudden went "Wait, what do you mean we only have two episodes left in the season?!"
Because some of the absences and plotting make sense if you were looking at a longer arc then they wound up getting. (i.e. having more episodes meaning you'd have more time to focus on others then get back to Zatanna's issues and such.)
And the last two episodes, although quite good, do come off as a bit...rushed.