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As long as you have work items created and your developers keep them up to date, you can use MS Project to calculate project budget usage in real-time; this helps the project manager to determine the progress in term of $ which is what client really care about. Note: To have this working properly, you need VSTS 2010 because it has better MS Project integration.
Judging how long a project will take is a difficult task as there are many factors to consider like resourcing, leave and blowouts.
Timesheets have always been the bane of developers, with them trying every excuse under the sun to avoid them and project managers trying everything to convince them to enter them.
Projects will change and deviate from the original scope – that is a given in software development. When a client sends you an urgent task (as per the order of importance rule) then you need to do it in the current Sprint.
This should rarely happen, as new features should be pushed back to the backlog, to be prioritised into the next Sprint, but sometimes the Product Owner will say that it's urgent and has to be done immediately.