Writer centipede one way we get terrible TV.
Like human centipede, Hollywood (and other) writers tend to just take other peoples stuff and slap it in their stuff. For example: you will see the main male character and female character fighting and then they make out and have sex. When you see that happen in a show your first thought should be "Oh god, please don't go there again" but then after that you have to ask how many writers this idea passed through, before the current TV show tried to get you to eat it. Was Shakespeare's Taming of the Shrew where this idea first popped up? Was it from older Greek plays? Either way that "angry > making out" thing has been ripped off a lot over the centuries.
There are so many other ideas and mechanisms that pop up in TV that are cliche's and tropes. In both cases if you are using them, what you are doing is using someone else's work, it is lazy and plagiarism. Just because an idea has been stolen so many time people cannot say where it was first created, doesn't mean if you use it you are not also stealing it. Just because someone else stole it doesn't make it OK for you to (two wrongs blah blah).
If you ideas are on TV tropes and have a bazillion citations.. uh oh. http://tvtropes.org/pmwiki/pmwiki.php/SoYouWantTo/WriteAShonenSeries

Well, the how does this happen?
Mirror neurons is the answer. These are created as you watch something happen and are responsible for "monkey see, monkey do". What this means is that when you come to any given point in a story, you are likely to replicate something you have already seen for what happens after that point.  What is the point of mirror neurons? All life is lazy, it is better to learn something from watching someone or something else do it than to spend calories figuring it out yourself. This is also there reason that people are most comfortable feeling about things rather than thinking about things, it is also what people are more comfortable not paying attention and answering things with rote knowledge. Paying attention and thinking requires more calories than feeling as rote learning and so is risky on an evolutionary level. As a species you only need a few thinkers who will provide rote learning to the rest. (At his point some of you who have turned to the dark side are saying "So for most people I can just pack a story full of emotional triggers and they will think 'This is great!'".. bad Jedi, no biscuit! Don't have those thoughts.)

OK so how do I deal with this?
Bad news: you will not be able to avoid it. Or at least will have a really hard time avoiding it.
What you can do is know that this will happen and watch out for when your brain tries to do it. Also learn as much about everything as possible, then have many people proof your stuff, to see if they catch stuff you didn't.
For characters it really helps if you can be very social, talk to everyone, have deep conversations and get to know them. Learn some psych, learn social engineering so you know how people work and you can make tangible characters and not card board cutouts. Also taking things from real live means they usually to not trace straight back to TV eps everyone has seen.

When it does happen, can you mask it? Take the cliche and mix it up until people do not spot it or for fun take it 180 degrees from where it always goes. Distract the reader so they do not notice what the other hand is doing.
Most of all, never tell yourself that your story is great (OMG, this is going to be awesome!). Ask what is wrong with it, dig for the wrongness and fix that, then dig for more. When you run out of wrong then have others dig. This is how science and good writing work. When no one can come up with wrong, you have a story that is lacking wrong and is hopefully enjoyable to boot.

If you do this all well, hopefully you will always be able to earn suspension of disbelief and maintain a hold on it.

What if I can't get my brain to do this or it is more effort than I want to spend? Then you have a bright future as a Hollywood writer. We shall await your next episode of Star Trek or The Flash. Just grab your bottle of paste (do not eat any of it, no matter how good it is. you do not want the other Hollywood writers calling you "paste eater") and some construction paper and make a collage of cliche's around your cardboard cut out characters.

I think its good to talk with your characters. in a sense, i've always done this and felt so natural. But it started by feeling characters that regardless if i thought were great or not, i can see them real people.

Sometimes when people do this, and i see examples of this, i tend to see typical discussions set up for the character rather than seeing a character have a real character.

Again, MN's are quite a new subject (around 20 or so years) and they're not fully understood. There's quite a few things we think they do. Generally though, i think it's safe to say that they're not responsible for our behaviour/or passing down behaviour, they're responsible for linking motor action and perceptual representation.

There's a nice minireview that goes over some of the research done in the last 20 or so years that's quite a light and nice read, called 'What we currently know about Mirror Neurons' done by Kilner & Lemon. Or Wikipedia might be useful, but it also seems to touch on other Psych theories like ToM, Autism and the likes. Not sure if Wiki would be too much of an overload, since it sounds like you've not read anything on them.

I'm not really sure what you're meaning by 'wiring', generally when i think of wiring i think of white matter since it's generally used to connect areas of the brain to each other.