There are at least two main problems that can be identified with regard to the federal budget process. One of these is more political and the other is more economic.
Politically, the major problem with the process is that it is too difficult to get a budget passed. The federal government often goes years without producing and passing a full-fledged budget. This is largely because it is so hard to get both houses of Congress and the president to agree on such a large bill. This tends to lead to a succession of stopgap measures that allow the government to keep running but prevent it from ever creating a long-range budget plan. This does not help the country at all.
Economically, the major problem with the budget process is that it is too vulnerable to the demands of special interests. A major problem in the US is the huge budget deficits that the government runs. One major reason for this is that every government program has a constituency that can bring pressure to bear during the budget process. The easiest thing for the politicians to do is to give all the interests what they want so that the budget can pass. This means that it is very difficult to ever reduce spending or to raise or reform taxes so as to put the country on a more stable financial footing.