The movie had an episodic plot, not the "strongest" kind but not in and of itself objectionable.
I'm not sure what you mean by "episodic" exactly. Could you clarify?
From my point of view, I would say the plot is weak principly because it relies on the boring and inconsistent plot device of Red Matter and a series of glaring and implausible coincidences in the pivotal sequence on Delta Vega.
To put it another way, I think the movie succeeds in spite of its plot and not because of it.
What is very heartening for me is the fact that the sequel should automatically have a better story since the reboot is over, the origin story is told, and time-travel from the Prime universe will presumably not be necessary.
I can't wait to see this crew, this ship and the new pacing and effects in a better story.