Pentax K-3 has a 24.0MP APS-C (23.5 x 15.6 mm ) sized CMOS sensor and features Prime III processor. On the other hand, Sony A99 II has a 42.0MP Full frame (35.9 x 24 mm ) sized BSI-CMOS sensor and features Bionz X processor.
Sony A99 II's sensor provides 18MP more than Pentax K-3's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Another similarity between these two cameras is that both Sony A99 II and Pentax K-3 sensors lack anti-alias (Low-Pass) filters. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moire occurring in certain scenes.
Below you can see the K-3 and A99 II sensor size comparison.
As seen above, Sony A99 II has a 2.4x Larger sensor area than Pentax K-3. Larger sensors give photographer more control on the depth of field and blurry background compared to smaller sensor when shot in same focal length and aperture.
DxOMark Sensor Scores
DxOMark is a benchmark that scientifically assesses image quality of camera sensors. It scores camera sensors for color depth (DXO Portrait), dynamic range (DXO Landscape) and low-light sensitivity (DXO Sports), and also gives them an overall score. Pentax K-3 and Sony A99 II sensors have been tested by DxO and the results show that A99 II has a better overall score of 92, 12 points higher compared to K-3's score of 80.