: What to do if I end up confused by my own plot because of 'trying to be original' or 'trying to make the story more deep'? Sometimes, I find myself in the dilemma that I come out with

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I think you are confused about "originality". Every super-spy movie is "original", but the plot is the same. Nearly every romantic comedy is original, but the plot is pretty formulaic.
What is original is the setting, the characters, their motivations, the complications. One rom-com about a break-up, that causes a girl to use the tickets that were supposed to be for her honeymoon to go feel sorry for herself in Paris, where she meets a rough but lovable laborer and understands she was really never in love with her fiance --- because she is in love now and has never felt THIS way before.
Or take Notting Hill: Julia Roberts plays a famous actress that encounters Hugh Grant, a small London bookstore owner. Complications are different and revolve around her fame (and his complete lack of it or experience with it). But the plot is the same; how do these two people destined to be in love for life ever get past themselves and their obstacles to be together?
Do not make your story confusing, if you can't keep track, readers (or more generally the audience) have no hope. Your originality is in you descriptions, your settings, your dialogue, the problems you create for them.
If you want a "twist", there is generally one, expertly woven into the narrative:

Cole Sear: I'm ready to tell you my secret now.
Dr. Malcolm Crowe: Okay.
Cole Sear: Come closer.
Cole Sear: I see dead people. They don't know they're dead.
Dr. Malcolm Crowe: Where are they?
Cole Sear: Everywhere.

This was early in the movie, and the strongest possible hint at the twist, but few people saw the twist coming. But it is ONE twist. It isn't too complicated. Crowe [Bruce Willis] is helping this psychic kid deal with a problem that is terrifying the kid, 90% of the story is exploring that problem and seeing how the kid grows to handle it.
A good twist like this is awesome, but don't pile twists on twists. One is enough, and you don't need any at all. "Kingsmen" is not much different than a 007 flick, or Taken flicks, or Die Hard flicks. The originality is in the heroes, the villains, their skill sets, the problems they face, their attitude, their motivations for risking their lives to save anything from a single girl up to everybody on Earth.

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Theme development should be natural.
The art of writing fiction is the art of building a world. It may be a very small world, such as a ride up an elevator with a character reflecting on his life. It may be a very large world such as J. R. R. Tolkein created in the Lord of the Rings trilogy and other stories set in Middle Earth. It may be somewhere in between. It is not going to be an original world, but it will be a world through your eyes. Why else do we read but to get the author's window on the world?
Fiction works which set out to prove a point or support a thesis are very rarely well received by modern audiences, who often view them as overly moralistic or trying to bash people over the head with a point. If you do have an idea in mind, such as questioning the sanity of certain types of people, try and build a world in which they will naturally demonstrate the fact that they aren't quite sane as most would describe sanity.
Originality is overrated.
Don't stress about being original. Just don't. First of all, if originality were really a big thing, genre fiction would have died out an age ago. Even in the world of literary fiction there is a lot of hashing and rehashing. Plus if you are confused by your own originality and you are the author, just try and picture a reader who didn't know what you are getting at figuring it all out. Just because Joyce's Ulysses is famous even though it was declared unreadable doesn't mean the rest of us should try and be James Joyce!

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Finish them anyway. You get good by writing; plotting alone isn't enough. And yeah, your first novel or two will probably be unpublishable. That's fine - those will be your practice novels. If you never write anything because they'll be less than perfect, I'm afraid you're likely not to write anything at all. Not only will finishing your imperfectly-plotted novels help hone a whole bunch of other writing skills, it will give you hands-on experience with translating a plot into a story - which is crucial to understanding how to write a plot to begin with. It will give you the sense of where the originality and freshness might still come in even in a familiar plot, and of how to add extra layers without devolving into cliche. Practice, practice, practice.
Don't pander to the imagined masses. It sounds like you're saying you've got Plot A that you yourself are perfectly happy with, but you've got the sense that Plot A "should" be more original/more meaningful. Don't bend yourself out of shape over what your novel "should" be like, particularly when you haven't written it yet. If you yourself feel that Plot A is terrific, then changing it in response to perceived criticism that you yourself don't understand and/or agree with is unlikely to be an improvement.
Most stories aren't very original. They really aren't. This may not be particularly inspiring, but it's kind of comforting to know you don't have to invent a new type of wheel. There's plenty of room for "familiar" stories with new characters, or new twists on old tropes, or just the joy of reading a story done well - even if it is similar to others we've read before.
Stories don't have to mean things. They really don't. If you've got a cool idea, something that excites you and would be interesting to write about, then why twist it into a "message" or a "meaning"? You're not writing an editorial, you're writing a story. In other words, things happening. What's wrong with letting 'em happen?
Your writing is more original and meaningful than you think it is. Although not necessarily in the ways you might expect. The unique thing about your writing is that its yours, and nobody else would write the same characters and events in quite the same way. You can bring originality and meaning into your stories, even without intentionally doing something to be deliberately original or meaningful. By pouring your self, your thoughts, your feelings, your observations and understanding of the world, into your work - you'll be doing something unique. By improving your craft - your skill at portrayal, your eye for detail, your intriguing cast, your gripping scenes - you'll be polishing up that unique aspect until, eventually, it shines. Shakespeare wasn't original, but he was damned good at what he did.

I guess my advice here boils down to saying: it sounds like you're worrying about this more than is warranted. I understand your difficulty, because you want your books to be original and meaningful - and isn't that why we read books to begin with? And it's true - your books might be cliche or incoherent enough that they'll be awful. But it's important to understand that these two values are not the be-all and end-all of writing, and they certainly shouldn't stop you from writing entirely. You've staked out where you want to get to - because you know you can write stories that will have everything you want.

Keep going. You'll get there. :)

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You're trying too hard.

Put the structure of your novel together. Don't worry if it's been done. It's all been done. There are something like forty plots in all human literature. Trust me, whatever you're doing, it's been done. "Boy gets girl, boy loses girl, boy gets girl back" is done twelve times a day and a few extra on Friday nights, but oddly, neither the romance novel business nor the chick-flick industry are collapsing. The point is to do it well.

Write the best novel you can. Have it edited repeatedly. Ask your editors to point out anything which seems painfully derivative, and focus your improvements there.

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Originality is generally overrated and never more so than in the case of a first-time novelist.

Think about it. Most published works achieve very little in the way of originality. You are trying to do something which is difficult i.e. sustain enthusiasm, concentration and some sort of narrative through-line for circa 50k words minimum. Now you want to write something the like of which the world has never seen into the bargain?

I mean the former task is foolish and difficult as it is. The latter is foolish and so difficult it is very nearly impossible.

My advice, for what it's worth, is to get some novels done first and worry about innovating in the novel form in your chosen language second. Or, more succinctly, don't run before you can walk.

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