the idea that you have power to change the structure of code and you should do it, keeps bothering you. What you should do?

Tread very carefully:

• Does the code in question have a good set of regression tests? After all, your "improvements" may introduce new bugs in working code. How will that news be received? Without the safety net of a comprehensive test suite, refactoring legacy code is suicide.
• How do you know your restructurings are "better" than the original code? Are you smarter than the original developers? Are you a better programmer? Do you understand the problem domain better? Do you have more time?

See also:

• Nobody Expects the Agile Imposition (Part VI): Architecture
• The Boy Scout Rule
• Strategies for maintenance of horrible code?