[I]t would tend to increase the complexity of the political machine, and to add a new spring to the government, the utility of which would at best be questionable . . . [it] might in practice be subject to a variety of casualties and inconveniences.
- Alexander Hamilton, Federalist 65 (on a separate body for Impeachments)
The most obvious source of delay in Government due to the Separation of Powers Principle as instituted in the Constitution is the Bicameral House - every law must be passed in identical form by two separate Legislative bodies, a requirement that allows few laws to emerge unscathed. Even in 1776, this notion was seen as counterproductive by an anonymous author, who wrote in "Four Letters on Interesting Subjects" that
The notion of checking by having different houses, has but little weight in it, when inquired into, and in all cases it tends to embarrass and prolong business; besides, what kind of checking is it that one house is to receive from another? or which is the house that is most to be trusted to? . . . That some kind of convenience might now and then arise from having two houses, is granted, and the same may be said of twenty houses; but the question is, whether such a mode would not produce more hurt than good. . . . a perpetual and dangerous opposition would be kept up, and no business be got through: Whereas, were there a large, equal, and annual representation in one house only, the different parties, by being thus blended together, would hear each others arguments, which advantage they cannot have if they sit in different houses. . . .
The chief convenience arising from two houses is, that the second may sometimes amend small imperfections which would otherwise pass; yet, there is nearly as much chance of their making alteration for the worse as the better; and the supposition that a single house may become arbitrary, can with more reason be said of two, because their strength is greater. Besides, when all the supposed advantages arising from two houses are put together, they do not appear to balance the disadvantage. A division in one house will not retard business, but serves rather to illustrate; but a difference between two houses may produce serious consequences. 
This warning, unfortunately, was not heeded by our Framers, even though Madison acknowledged that "this complicated check on legislation may in some instances be injurious as well as beneficial . . . " Over time, a Committee and Seniority System has been created in both houses of Congress which has exacerbated the latent defects of Bicameralism. Under our Bicameral System as it exists in the 20th Century, the delay has been compounded in a way our anonymous author could not have contemplated:
In order for the average bill to become a law it must be: (1) introduced in both the House of Representatives and the Senate; (2) referred by both houses to separate committees where hearings are held and recommendations are made; (3) debated and passed in both chambers; (4) sent to a conference committee if the versions passed in separate houses are different; (5) approved by each house; and (6) signed into law by the president. Some bills, which overlap into more than one committee jurisdiction in each house or must be sent to subcommittees, have even more obstacles to final passage.
The passage of legislation is extremely difficult under such a decentralized system. The multiple decision points through which a bill must pass require majority coalitions at each gate to push the measure along. There is a complex division of labor in Congress. Responsibilities for specific policy areas are delegated among numerous committees and subcommittees. There are 269 committees and subcommittees in both houses of Congress. Broader issues, like the national defense, education and health care are divided into smaller subissue categories for committee consideration. . . .
The committees decide which bills will be reported to the floor for debate and which will be placed on the back burner of the congressional agenda. Favorable committee reports do not necessarily ensure the passage of the bill on the floor, but the more favorable the report from committee, the greater the probability for passage. . . .
In the Eighty-ninth Congress (1965-1967), 26,566 measures were introduced, 4,200 were reported from committee and 810 became public law. A similar trend continued in the Ninety-seventh Congress: although fewer measures were introduced (only 13,240), 1,877 were reported from committee and 473 became public law. Thus, the committee system as a gatekeeper of what is debated and what is not debated remains extremely important . . . 
As Greenberg (1986) noted, confirming the anonymous author of 1776, the Bicameral System inevitably led to the postponement of action, and has even changed the nature of the legislation ultimately passed. The medium doesn't allow every message:
[T]he bicameral nature of Congress and its contrasting constituency bases [Districts vs. States] not only serve to slow down the pace of legislation but also significantly decrease the probability that any general purpose legislation will manage to wind its way to completion. These elements of the constitutional organization of Congress make it halting, conservative, and indecisive. The Constitution further contributes to these characteristics by specifying that only one-third of the Senate shall be up for election at any one time, helping to insulate that body from the tides of popular sentiment. By its constitutional organization, then, Congress faces barriers to decisive, popular, and unified action. 
While the Framers approved Bicameralism, they did so with no empirical evidence of its ultimate effects, ultimate effects which were, in fact, seen by them as negative. For example, the result of the Bicameral process was an enfeeblement of Government, and feeble Government was seen as bad Government. As Hamilton stated in Federalist 70, "A feeble execution is but another phrase for a bad execution; and a government ill executed, whatever it may be in theory, must be in practice a bad government." Feeble Government, like a toothless watchdog, would bite neither mailmen nor burglars. What Hamilton wrote in a different context applies equally well to the Bicameral System: "The most to be expected from the generality of men, in such a situation, is the negative merit of not doing harm, instead of the positive merit of doing good."
"The positive merit of doing good" was made virtually impossible because of an institutionalized and debilitating delay, a delay which was dangerous even in 1787, a far more relaxed time. As Jay stated in Federalist 64,
They who have turned their attention to the affairs of men, must have perceived that there are tides in them; tides very irregular in their duration, strength, and direction, and seldom found to run twice exactly in the same manner or measure. To discern and to profit by these tides in national affairs is the business of those who preside over them; and they who have had much experience on this head inform us, that there frequently are occasions when days, nay, even when hours, are precious.
There could be no doubt that the Legislative process, stodgy by nature, would be rendered even stodgier by the Bicameral requirement. According to Justice William O. Douglas, "Legislative power . . . is slower to exercise [than Executive power]. There must be delay while the ponderous machinery of committees, hearings, and debates is put into motion. That takes time; and while the Congress slowly moves into action, the emergency may take its toll." Delay feeds vicious circles, which are vicious enough without help from Government. Unsolved problems mount. A failure to combat drug abuse leads to crack addiction. Crack addiction leads to crack babies. The existence of crack babies leads to a diversion of medical resources to help the babies. In turn, resources need to be diverted to schools to help these children, many of whom are brain-damaged, blind, or otherwise physically or mentally debilitated. Thus, money that could have been used to create positive effects is wasted in attempting to counter negative effects. What most people would see as insane is inevitable, because in Washington, D.C., structural procrastination impedes fundamental action:
A criticism often leveled at the U.S. Congress is its inability to enact legislation concerned with pressing national problems without long, arduous delays. It is not unusual for Congress to adjourn after a long session without having dealt with some urgent matter before it. In past years it has failed, for example, to pass a fiscal year appropriations bill until months after the date when the actual fiscal year began.
This lack of action handicaps orderly administration. It is not uncommon for Congress to approve minor, nondivisive measures in every session; moreover, in crises it can act quickly. But often it is unable or unwilling to act on pressing problems unless they reach a crisis stage. . . . 
Hazlitt (1942) understood that institutionalizing delay because it was occasionally beneficial was like refusing to teach people to think because some would think about committing crimes: "A nation can erect a complicated set of hurdles and barriers to compel itself to delay decisions, but . . . [b]y the obstacles it erects, it discourages itself from making any new decision, regardless of its merits. The self-erected barriers tend to bias its decision unduly against . . . proposed change." And Hamilton's fears that "the positive merit of doing good" would be in jeopardy have come to fruition. Today, a permanent stasis is apparent in Congress. As Representative Romano L. Mazzoli (D-KY) stated, "There's a frustration level. It doesn't seem like any problem is ever solved around here."
Thus, the first defect of the Separation of Powers Principle as instituted in the Constitution is that it creates delay in the face of a necessity for action. But that's only the first problem.
END PART 6: TO BE CONTINUEDFOOTNOTES
 Federalist 65, p. 334 (Hamilton).
 "Four Letters on Interesting Subjects," 1776, 1 Founders' Constitution 638.