I have, in addition, introduced a new method of philosophizing on the basis of numbers. -- Pico della Mirandola, Oration on the Dignity of Man
Wolfgang Pauli, in addition of being a Nobelized physicist, was most interested in the mental and psychological processes that make scientific discoveries possible. In a book co-authored with C.G. Jung, The Interpretation of Nature and the Psyche, he studies how Johannes Kepler discovered his three laws. By looking at the original texts of Kepler, who was a strict protestant, Pauli shows that the image that Kepler had of the Trinity led him to accept the Copernician heliocentrism, and to invent the idea that the movements of the planets could be measured and mathematically described.
The main enemy of Kepler was Robert Fludd, an English physician and astrologer. Fludd had a background in alchemy, kabbalah and mysticism. For him, the heavens (the macrocosm) was the reflection of the human body (the microcosm), and vice-versa: consequently, applying mathematical rules to the movements of planets was implying a negation of free will. (It's to be noted at this point that both Kepler and Fludd believed that planets were living beings.)
The same gap between Fludd's and Kepler's presuppositions can be seen on their approach to astrology. Fludd believed that astrology worked because of the mystical correspondence between heavens and earth. Kepler supposes action on the human mind induced by remote sources of light placed at certain angles -- the same angles that appear in Kepler's second law. As Pauli notes, Kepler's thesis is experimentally verifiable, but Kepler didn't seem to think that, if he his correct about astrology, artificial sources of light would have the same effect. Here too, Kepler completely externalizes the physical processes, something that Fludd refuses to do on religious grounds.
It's remarkable to note that Fludd's conceptions made him refuse Kepler's approach to astronomy, but enabled him to correctly discover the principle of blood circulation. That is, as the human body is like the heavens, where planets revolve around the Sun, image of God, then in the body blood must revolve around the heart, where is located the Soul, image of God. Or at least that's how Fludd saw it.
Even with false assumptions, both men made science advance. The conclusion of Pauli somehow was that, while all assumptions need to be scrutinized with skepticism, only the results will validate a scientific theory; but that those assumptions are precisely what makes the scientists creative. So, what kind of assumptions led to Pauli's Exclusion Principle?