Currently the axis and tooltip number formats for variables are linked. Changing the format of one necessarily changes the other. I suggest they be un-linked and separately controllable.
Use case: You are plotting sales on the order of several million dollars. By default Tableau labels your axis with full dollar amounts: $1,000,000.00, $2,000,000.00 etc. This is hard to read and takes up a lot of space. You go to format the axis, switch the units to $M, and reduce it to 1 decimal point. The axis is now more condensed and user friendly, but your tooltips are now less useful - they are also rounding to 1 decimal point.
Note: the following is a duplicate idea and it's score should be included in this score - http://community.tableau.com/ideas/4479