All season long, the "Alternate Timeline" due to the nuke was totally consistent. The odd bits (Jack's son, etc) could easily be explained away as results of Jacob's influence being removes.

Suddenly in the last episode everyone who had their memories of the other timeline returned to them started acting all wise and knowing; all vague smiles and soft words. Because someone finally told the actors they were in Heaven.

If it was heaven/vaguely-nondemonimation-afterlife now we have to scramble and wrack our brains to explain all the wierd stuff... why was Nadia married to Sayid's brother. Why wasn't Eko in it? Why was there a sunken island in Purgatory? Why does Jack have a son? Why why why why.

Adding a whole new layer to the fictional reality 4 minutes before the final credits isn't a briliant and emotionally touching conclusion to me.