Since the whole story devolved down to: MIB vs Jacob, pretty much everything to do with the Dharma initiative, the others from season 3, and the freighter from season 4 ends up being filler.
IF the freighter assault would have contributed to MIB's season 6 plan, it wouldn't have been filler.
IF the others kidnapping Walt & Jack et al. would have contributed to Jacob thwarting MIB's plan it wouldn't have been filler.
IF the Dharma initiative would have added anything to the MIB/Jacob conflict it wouldn't have been filler.
This is why the final season and the finale make 75% of lost pointless.