I actually agree with you that for a last bastion of humanity, Zion was a bit cold... not somewhere you'd call home.
Personally I count the exploration of the relationship between Neo and Trinity among the unnecessary side-plots. If it had been done more elegantly it could have added something, but the story didn't really need it. Also, I think Trinity's
Spoiler:initial death would have been a more dignified end than her ultimate demise in Revolutions. I think her dying there and then sans resurrection would have been more powerful and would have added more weight to Neo's final solitary journey.
What I liked was the interplay between Neo, Smith, the Oracle and the Architect and the story that developed from that. It's too bad Gloria Foster wasn't there for Revolutions... and Tank for both sequels. He was cool. The whole thing with Link and his wife didn't really grab me.
As for the battery thing, I'm OK with suspending disbelief on that.
At the end of the day I think they're a flawed but still fitting conclusion to the story.
