Exciting but deeply problematic finale

This finale had many good elements and was tense and gripping. But a lot of the plot details were sloppy and fall apart if you think about them at all. (I won't use the dreaded "plot hole" terminology, as I know it is highly controversial around here.) Some examples I jotted down while watching:

Why would the GSC not have that building guarded with Humanics? Later Lucy swapped in Humanics, but it's silly that it took their almost being breached to do so.

Charlie's apartment seems like a poor choice for the rebel HQ given that Lucy is totally onto Charlie. And this is proven by the fact that the fake Molly is able to find JD there. Why didn't they go back to JD's special hideout? And then why weren't any Humanics stationed at the apartment to wait for the real Molly to return?

As badass as Humanics are, they sure didn't get the programming instructions for finishing off the enemy. First at the hybrid hideout, and then now with JD, they sure give humans and hybrids lots of extra chances.

And indeed, they do come back but too late. Closing the barn door after the cow got out.

TAALR didn't station any Humanics to guard his server?

Here we go, the ol' "which one do I shoot?" dilemma. It's been done many times, but it's a good plot device so I don't blame them. I do have to question though why the real Molly didn't change her clothes before going in.

--------
My top 250: http://www.flickchart.com/Charts.aspx?user=SlackerInc&perpage=250