I seem to recall that 30 or 40 years ago, most federal budgets were passed department-by-department.
I believe it was when Democrats controlled Congress and the president was Reagan (or maybe it was Nixon) the DEMOCRATS decided to create an omnibus budget based on their theory that the president wouldn't dare veto a budget that was full of Democrat pork if he'd also be vetoing defense and health/human services.
As I recall, most of the press at that time declared that was a mistake that would lead to budget crises, as indeed it has.
And now the Democrats are angry that the GOP House has effectively proposed going back to department-by-department budgeting.
Of course, there has been no real budget since Obama took office, but who's counting?