That's a pretty poor analogy. It's more like, every time you fill your car up with gas you have to do an oil/filter change and rotate the tires. Why?
Other jailbreak versions allow you to do so without restoring the phone and having to reinstall/reset all of your preferences/settings.
Actually, it's a great analogy. Just like the Ferrari is a more powerful car than the Ford, PwnageTool is a far more powerful tool than either Star, Greenpois0n, or Limera1n. And just like you need a manual transmission to harness the Ferrari's power, the power of PwnageTool requires a restore. It's not a flaw, but a feature which is the very essence of the vehicle/application.
PwnageTool is not like other jailbreak tools. Its purpose is not merely to jailbreak your phone, but to ensure your ability to jailbreak your phone
forever. Unlike other tools, it is not good only for a single firmware version; once your phone has been pwned, you will be able to upgrade to any future version using a custom firmware without the need to wait for new exploits to be found and developed and without risking your unlock with a baseband upgrade. It does this by using methods that are fundamentally different from any other jailbreak tool. These methods, which require a restore, are not a flaw in the design, but a
feature of it; it is that feature which gives PwnageTool its power.
By all means, if all you're interested in is jailbreaking your device on the current firmware, use another tool. Nobody is forcing you to use PwnageTool. In fact, for you PwnageTool is probably a massive overkill. But to complain about PwnageTool requiring a restore is to completely misunderstand its nature and purpose.