I work on a project that was a ground up redesign, except for one small (but one of the most important features for our customers) that was ported to the new system. In the years since the team working on the ported part has been given time to make their code better. I have concluded that we could have in place refactored the old code to the new system and been fully functional the whole time for much less cost.

The new system is clearly better than the old one. If we had refactored in place we wouldn't have the same system as we have now. With the benefit of hindsight, I can now see some places in the new system that are not working as well as hoped and we are working on a plan to refactor those parts in place to something better.