Sounds like a great idea! I also have thought for many years about writing a fantasy or sci-fi novel that could have on readers the kind of impact that The Matrix film had. So I say, go for it!
Here is my piece of advice:
1. Start thinking about a plot that would illustrate your philosophical ideas: these ideas should be
showed in the actual plot, not just expressed by the characters in the dialogue (although a few good hints in the dialogue can obviously help). The Matrix is a perfect example of this: it has terrible dialogue, but a spectacular and mind-blowing plot. That's where its power resides.
Thinking out this plot is the most difficult and crucial part of creating your novel. But it can also be the most fascinating and rewarding.
2. Once you have a good plot that fleshes out your philosophical ideas (or your philosophical questions, which would be even better), you need good characters. Characters that your readers will care about. The most amazing plot will fall flat if your characters aren't up to the task. Remember that you are writing a novel, not a movie script. You can't rely on the carisma of some famous actor like Keanu Reeves (an absolute star, imho). There are many books that teach you how to "flesh out" your characters, but in the end I feel it all comes down to having a deep understanding of human psychology, and that can only start with understanding yourself. Deeply.
3. And this takes me to the discussion about the classics of literature: Cervantes, Tolstoy, Dostoevsky... These are classics because of the depth of their characters. (Other classics like Hemingway or James Joyce are more so because of the quality of their narrative voice, but I won't go there now.) And they are never boring. I just read Dostoevsky's
The Idiot and boy, was that a page-turner! More addictive than any stupid best-seller I ever read (I also read some of those, yes). There have been famous books like Thomas Mann's
The Magic Mountain that consist almost exclusively of interminable philosophical dialogues (or sometimes monologues), but that's not what you want: those kind of books are the definition of "boring" for an average reader. So again, I recommend you express your philosophy through the action and the interactions between the characters, not the dialogue.
4. Some writers that have tried this kind of thing (expressing philosophical ideas through popular fantasy or sci-fi novels): George Orwell, Aldous Huxley, Colin Wilson, Ursula K. Le Guin, Frank Herbert, Philip K. Dick... the list is endless. Actually, most great sci-fi writers ground their works on deep philosophical questions. Outside sci-fi you have writers like Hermann Hesse... There must be others, but they don't come to my mind right now. I think most philosophically minded novelists have always tended towards science-fiction or fantasy. An early example is Jonathan Swift's
Gulliver's Travels.
Anyway, I hope this helps! Even if you never get to publish or even finish your novel you will have great fun and learn a lot, I guarantee. I just finished my "masterpiece", which is exactly like that, a "The Matrix"-like work of fiction, and I'm feeling pretty happy and proud of my achievement.
:)