Some factors (not exhaustive ) to consider (this is a comparison strictly between the big 3):
Most weeks at #1:
1-Federer (310) 2-Djokovic (260) 3-Nadal (196)
Most year-ends at #1:
1-Federer (5) 2-Djokovic (5) 3-Nadal (4) - used overall # of weeks to break tie
Most titles overall:
1-Federer (102) 2-Nadal (82) 3-Djokovic (75)
Most tier 1 titles (slams/WTF/masters combined):
1-Federer (54) 2-Djokovic (54) 3-Nadal (52)
Most slams overall:
1-Federer (20) 2-Nadal (18) 3-Djokovic (16)
Most titles at every slam :
1-Federer (8-6-5-1) 2-Djokovic (7-5-3-1) 3-Nadal (12-3-2-1)
Most WTFs:
1-Federer (6) 2-Djokovic (5) 3-Nadal (0)
Most masters:
1-Nadal (34) 2-Djokovic (33) 3-Federer (28)
Most of the 9:
1-Djokovic (9) 2-Nadal (7) 3-Federer (7) - used overall # masters to break tie
Most dominant season:
1-Djokovic (2015: 3 slams + WTF + 6 masters) 2-Federer (2006: 3 slams + WTF + 4 masters) 3-Nadal
Most consistency/longevity:
1-Federer (15 seasons of winning at least 1 tier1) - 2-Nadal (13) 3-Djokovic (10)
Best winning % overall:
1-Nadal (83) 2-Djokovic (82.7) 3-Federer (82.2)
Highest winning % across surfaces:
1-Djokovic (G84.1-H84-C79.6) - 2-Federer (G87.4-H83.7-C76.1) - 3-Nadal (C91.8-G78-H77.3)
Best head to head vs other big 3:
1-Djokovic (26-22F/28-26N) 2-Nadal (24-16F) 3-Federer
Best head to head vs top 10:
1-Djokovic (68.6) 2-Nadal (65.2) 3-Federer (65)
The ones that Fed is most at risk of losing are weeks at #1, year ends at #1 and tier 1 titles (to Djoko) + slams to Nadal.
Nadal and Djoko are a toss for masters
(I could just count slams instead but seems too boring, sorry
)