Pay For Meat With Candy

If the system commissioners are different from the system users, and you have to keep both happy, you can pay for refactoring and upgrades in the user's eyes with a stream of cosmetic and usability items that don't bulk the work too much.

The users buy into the project more because they (a) know you are doing something major the commissioners want, and (b) see that in spite of that you will take the time to help them with little things that make their work more pleasant. Their visibility into the process is important.