There are three acts in Metropolis Zone because the artist in charge, Tom Payne, was also working on a second level which was removed from the game because of a lack of time. An industrial zone with moving platforms, giant spinning cylinders and teleport machines (which were introduced in the Scrap Brain Zone in the original game) means that Sonic has to stay light on his feet. In addition, he has to face frequent lava pits, menacing crushers, and the three most dangerous badniks in the game. Thus, it makes for a rather difficult zone.
When Robotnik appears at the end of Act 3, he descends down with several spinning satellites protecting his mini ship. After a few moments dodging these orbs, Robotnik will be vulnerable for just a second. If Sonic attacks him at this point Robotnik will fire off one of the satellites which transforms into a replica of himself. These can then be destroyed with ease. When his supply of satellites has been exhausted Robotnik will fire of laser beams at Sonic which can easily be avoided and leave the hedgehog one remaining shot at the mad scientist.
If you want to do it quicker, you will need precise timing and some luck. Notice that when Robotnik spins his shield, he always leaves one side vulnerable. Those sides change quickly, but one of them can always be attacked. Which means that if you're brave, you may simply deck him from below when he comes down. If you're going to do it this way, you should have quite some rings for backup measures, as you'll probably get hit a lot doing this.