A couple of general points:
Automating shield functions sounds like a sensible thing to do in general. However, we have reason to think that key facts are being hidden from us in this respect, facts that dictate such counterintuitive procedures as keeping shields down till the very last moment even in situations of confirmed threat. Apparently, keeping shields up is a bad
thing in general! For what reason, we don't know; perhaps they consume too much power, perhaps they reduce sensor efficiency by 97%, perhaps their glow makes long and medium range targeting significantly easier for the enemy. But clearly some sort of a regulation or bit of training, conventional wisdom, whatever, is in place to keep starship skippers from allowing their shields to pop up willy-nilly, and blindly contradicting that idea would be "anti-Trek".
Commbadges seem to play a somewhat mysterious role in transporting, too. We have this odd practice of the "Three to beam up!" commands in situations where the exact identities and positioning of said three is crucial and supposedly unknown to the faraway transporter operator. Are we to assume that the transporter operator has an accurate view of what is going on ("There's a canyon to the left" etc.), and the commands and communicators are essentially superfluous? This would seem to fly in the face of the plot element where removal of communicators categorically prevents beam-up. Rather, it would seem that the communicator is the key element that allows the transporter operator to accurately observe who or what is being beamed up, and "There's a canyon to the left" is the best he can do without the communicators. Any attempt to make do without the communicators would then be "anti-Trek".
Also, constant tracking of people in general appears to be so rarely done that there probably are laws against it, even within Starfleet. Either that, or then it's trivially easy for a villain or a privacy-minded person of even moderate skills to thwart tracking, so the heroes never assume they would have a means to track or even backtrack.
It doesn't need to work for 1014 people at a time, only those few who decide to ditch their badges and go rogue, for a temporary period of time.
But evidently all people take off their badges at least once a day. And they don't want to get tracked on such an occasion.
I'm implying they're like all computers... Garbage in, garbage out.
To the contrary, Trek computers tend to exhibit considerable initiative and intelligence - second-guessing their users often enough, answering unasked questions, refusing to answer asked questions, interrupting, interpreting...
They behave as if they were programmed by 1980's television writers or something!