Budget visible along the way, not after the fact
A project has an hour or amount budget, and usage is counted from time entries as you go. An overrun is visible while you can still react - talk to the client, move the scope, ask for an annex. After the fact all that is left is deciding who will pay for it. With the Employee settlements module the budget burn also shows the team cost, with Client settlements the revenue, and with both the margin.
A plan, not just a list of tasks
Milestones show the progress of their tasks and mark the late ones. Task dependencies say what is waiting for what, and an attempt to close a loop is refused straight away. A project that worked well can be saved as a template - tasks and milestones as days from the start - and the next one built from it.
The project team, not the whole agency
Specific people join the project, and they are the ones who see its tasks, files and chat channel. That way in a larger agency not everyone sees everything, and the project's client does not come across other clients' matters.