Thinking ahead, before you have done the experiment: II some "Nice" packets ought to have shorter round-trip times and other "Ugly" packets ought to take much longer, then there is a big advantage in doing a paired test. So design the experiment to keep track of pairs.
If you have already done the experiment and happened to keep track of pairs: You might see if Protocol A scores are correlated with their respective Protocol B scores. If there is significant correlation, the advantage of doing a paired test may be considerable.
If you have data with no tracking of A/B pairs: Then you'll have to do a 2-sample test.
Note: Whether these are paired t vs 2-sample t, depends on whether the data are normal. But here are ways to do both paired tests and tests with two (independent) samples for non-normal data.