Instead of recreating the wheel, here are some pretty good reasons why you need to do a break-in on any engine, be it a motorcycle or a car. I found it on this page. I don't necessarily agree with everything the person says on the page, so I'll leave the rest of the reading up to you.
The What:
Every new engine has internal components that must be "worn-in". This "wearing-in" of components is what's known as "break-in". The main components that need to be broken-in/worn-in are the valves, the cylinder bore, and the piston rings. These components must be worn-in so that they mate properly with the surfaces they will interact with over the life of the engine.
NOTE: At this point on the page the author states about valves not sealing correctly if not broke-in right. I will differ with him somewhat here as the way you get the valves to seal is to properly lap them prior to putting the head back on the engine. If lapping isn't done correctly, the valve will never seal and you'll lose all kinds of cylinder pressure while running the engine ... this is so for a car engine, I'm assuming it is exactly the same for a motorcycle.
The Cylinder Bore and Piston Rings -
The cylinder bore of a new engine is somewhat rough, and the piston rings are not properly mated to the cylinder bore. Some of the cylinder bore roughness must be worn down and smoothed out in order to create just the right amount of seal between the bore and the piston rings. Also the rings must be worn in correctly to mate with the cylinder bores. This process must happen properly in order to create the right kind of seal that will keep the combustion gases separated from the engine oil, and vice versa. Furthermore, if this wearing-in process does not happen correctly, the cylinder bore walls can glaze over, which will cause a lack of lubrication between the cylinder bore and piston rings, leading to overheating, a loss of performance, premature wear, and a loss of reliability. If this glazing does occur, the only way this problem can be corrected is for the engine to be torn down, the cylinder bores re-honed, and new piston rings installed, after which they must of course be broken in correctly, or it must be done all over again until it is. So you see how crucial proper break-in of these components actually is.
The Why:
Quite simply, these engine components must be properly "worn-in" to ensure good performance, reliability, and longevity; it's really just that simple. If these parts are not worn-in correctly there will be a loss of performance in every way. There will be a loss of power, poor fuel efficiency, increased oil consumption (burning oil), among other problems.
I'd also like to point out, in flat tappet engines, you need to vary the engine speed at 1500-2000 rpm for about 20 or you will flatten cam lobes out. You do this so the cam lobes and the base of the lifters will get a sympathetic wear pattern to them. If you let your engine idle upon first startup, you will wear through the hard metal surface of the cam lobe and lifter face and you will wipe out your cam. Roller cam engines do not have this same problem.
There is a huge amount of controversy over the how do you break in an engine out there. There are two trains of thought on this: 1) break it in as the manufacturer recommends so as to maintain warranty; 2) run it like you stole it. I don't completely agree with the stole it method, but believe the better way to do it is hard rather than soft.
By far the best method I've seen is this one. Not only has the guy documented exactly what he does, but exactly why he does it (with pictures to show you the difference). Basically, he is saying do the following:
Do Three 1/2 Throttle dyno runs from
40% - 60% of your engine's max rpm
Let it Cool Down For About 15 Minutes
Do Three 3/4 Throttle dyno runs from
40% - 80% of your engine's max rpm
Let it Cool Down For About 15 Minutes
Do Three Full Throttle dyno runs from
30% - 100% of your engine's max rpm
Let it Cool Down For About 15 Minutes
You'll notice he's talking about doing the runs on a dyno. You can do this on the street as well, but it works better in a controlled environment like a dyno, or a race track, or wide open country roads. A couple of the key things you want to remember is not to lug the engine and let the engine decelerate on its own (creating a large amount of vacuum in the cylinder). If done on the street, you can vary what gear your running in to complete the above sequence. On the dyno, you need to be running it in a higher gear because you don't have the load that you do on the engine from wind forces.
One of the key things which is stated on the page is that with the proper break-in, it can be worth 2-10% more power out of the engine. It will also help for the longevity of the engine. Yes, the engine will run, but it won't run as good as it could have, won't last as long as it could have, and you'll usually end up burning oil and having blow-by a lot earlier than would otherwise be expected.
If you choose to use this method for break-in, please read the page in its entirety. There is a lot of good information on there.
