the two could be compared if phelps had only swam the 50 and the 100.........phelps swam everything. Bolt would have to compete in the 100, 200, 400, 800 etc. to have the same overall round out of phelps.
Honestly, the only track and field athlete you can compare to phelps is the decathlete. The american who won the decathlon could probably held up as the greatest athlete in the world due to the variety of events these guys have to compete in and the timeframe their given. They are the only ones' that can compete with what phelps did. Bolt is the fastest man on the planet in shoes, hands down. But he's all legs........does he exhibit the same overall full body athleticism as a decathlete or a swimmer?.........no
Bolt is the flashier athlete though and track/field is more interesting to watch than swimming........hence we'll remember him jogging backwards across the line in the 100 more than we'll remember phelps's runs.