Firstly, all the possible independent variables mentioned are continuous variables. Gravity is a variable often overlooked by many simply because in the lab it can't be changed. Air resistance is often not considered because most pendulum bobs are small and do not produce much air resistance. The air resistance could be changed considerably by having a large light-weight bob and this would cause an interesting change to the swing of the pendulum. You just have to imagine what would happen if you tied a balloon to the end of the string instead of a small heavy object.
The mass of the bob does not have much effect on the time. It is still interesting to investigate it and see what results you get. The hardest part is designing a method where you change the weight without changing the centre of gravity of the pendulum. A small shift in the centre of gravity changes the length of the pendulum, and we know that changing this has a big effect on the time of swing. It is still difficult to produce a prediction that explains why the time doesn't change.
For small swings there is very little change to the time for each swing. You need very accurate equipment to detect the small changes and are not likely to do this with a stopwatch. Again, writing a prediction to explain this is difficult.
Notice that several possible dependent variables have not been mentioned at all. For example, it would be interesting to investigate how the speed or acceleration of the pendulum varies throughout the swing. These would involve different measurement techniques and would require more than a simple stopwatch! One example could be to investigate how the maximum speed of the pendulum changes as you change the size of the swing.