Let’s back up a bit before any large funding request comes to Congress. In order for any large-scale project to occur, first the Executive Branch of the government must propose it. That can take many, many years to happen. The program managers, scientists and engineers must first get their own agencies (like a national lab or something) to support the program, generally by explaining how the program is achievable, affordable, and useful. Then the agencies must take the proposals to the cabinet departments and get their support; then the departments must take the proposals to the Office of Management and Budget in the White House after that.
Getting all of these ducks lined up to support something big is no small feat at all. Devoting more money to program X generally means less money for program Y, not to mention substantive criticism of the project. Every type of bureaucrat you can imagine gets a say somehow: from scientist bureaucrats weighing in on the substance, to budget bureaucrats weighing in on the cost, to leadership bureaucrats questioning why it needs to be done at all. Those arguments happen at every level (agency, department, OMB, etc.) of the discussions on whether or not the project should be pursued. Of course, getting high-level buy in is extremely helpful. For example, the National Ignition Facility was helped along by the end of the Cold War and the view of the President and other government leaders that nuclear weapons testing should be curtailed and perhaps eliminated. Again, this process isn’t usually played out over weeks or months, we can be talking many years to gather this sort of support.
Once the Executive Branch has blessed something, taking it to Congress is the next step. The President submits a budget every February, so again, if a program doesn’t make it into one budget proposal, everything has to wait for another year. It typically takes Congress eight or so months to examine the budget and approve it. But, as you can expect, by the time Congress sees the budget, the various committees and staffs will not be surprised when a big program appears in it. That’s because that big project will have been in the works for years, and none of the discussions within the Executive Branch will really be secret. Big programs tend to get the press interested, and heck, the President may even mention it in the State of the Union address.
Once Congress sees the budget proposal, it’s more or less the same process as what was done within the Executive Branch, except it is a separate a co-equal branch of government asking the questions. Will this succeed? How much will it cost? Will it take away from other programs that we support? Where is it going to be located? Is there strong political concerns about the nature of the program?
As a rule of thumb, Congress doesn’t really change the President’s budget proposals all that much. Over time, the Executive Branch probably gets 90-95 percent of what it wants… but the Executive Branch can change its mind on what it wants as it gauges support and opposition in Congress. In my opinion, I’d say the work that is done to gather support for a big R&D program in the Executive Branch is a lot more laborious than what goes into convincing Congress to support the program.
Now, there are many variations on this process. Sometimes research projects are pushed by Congress as opposed to being formulated in the Executive Branch; the one example that comes to mind is the 1980’s research on turning coal into liquid fuels or clean-coal power technologies have powerful support from coal-state congressmen that really pushed those initiatives. But over the time it takes to conceive, design, and execute a large project like we’re talking about, political winds in Congress tend to shift. Senators lose re-election, control of Congress changes now and then, and so on – whereas the bureaucracy remains the bureaucracy, and despite changes in agency leadership and presidents, it can be harder for the bureaucracy to change course than for political leaders to change their mind. That’s again why getting Executive Branch support for a program tends to require more work.