With the 990cc era of MotoGP now complete, the manufacturers were somewhat more forthcoming than usual with details about their machines at the end of the season. In particular, Yamaha and Honda elaborated on certain aspects of the M1's and RC211V's development. In general, the development of those two models have been more evolutionary than radical, with each iteration changing subtly over the course of MotoGP's first five years.
In a presentation given after the final Grand Prix in '06, Koichi Tsuji, the project leader for Yamaha's YZR-M1, described three distinct but overlapping developmental objectives: the chassis, the engine and the EMS (engine-management system). Specifically, the chassis needs to be designed for maximum agility, the engine for the best balance of power and drivability, and the EMS for a "direct natural feeling" to the rider. Honda's technical bulletins for the RC211V over the years reveal a pattern similar to the details given in the M1 presentation, with both showing more of an emphasis on electronic controls and rider aids over the course of MotoGP's first years.
The Ducati Desmosedici's frame has no cross-members at the rear. With its Unit Pro-Link-like rear suspension, the shock mounts to the swingarm at the top, and the bottom linkage attaches directly to the engine. Just as with the company's road bikes, the swingarm pivots in the engine cases rather than the frame. Isolating the rear-suspension loads in this manner would allow engineers to easier tailor the frame's stiffness characteristics in various directions, an important consideration for absorbing bumps when the bikes are leaned over in a turn.
With each improvement in tire grip, the bikes are capable of ever-more-aggressive lean angles, and the frame and swingarm become more responsible for absorbing midcorner bumps. This is accomplished by designing in a certain amount of flex, as opposed to building a frame or swingarm as stiff as ultimately possible. Chassis stiffness is generally defined in three planes: vertical, lateral and torsional. Vertical stiffness must be strong enough to handle braking loads, whereas torsional and lateral rigidity must be lower to allow the chassis to flex and absorb bumps. This has led to frames and swingarms with taller and thinner sections as time goes on, with some appearing surprisingly flimsy. For '06, Yamaha removed the cross-member to which the rear shock mounts and attached the shock directly to the engine. While this change did alter the characteristics of the frame, feeding the suspension loads into the engine would also allow the frame to be better "tuned" to achieve a specific characteristic. The RC211V's Unit Pro-Link design offers similar benefits, as does the Ducati Desmosedici's rear suspension layout, which is similar to the Honda's.
This angle of the '06 original and new-generation Honda RC211V frames shows the importance of frame and swingarm stiffness in various directions. The individual spars are very tall, for good stiffness in the vertical direction, but quite thin to allow the chassis to absorb bumps when leaned over. The overhead naked shot of the M1 in Kunitsugu's MotoGP Rides story likewise shows the narrowness of the Yamaha's frame rails.
Another aspect of the chassis design is mass centralization, and this is mentioned consistently by all the manufacturers in their press materials. The closer the bulk of a motorcycle's mass is to the center of gravity, the easier it is for the rider to turn the bike. Over the course of the first years of MotoGP, this has been most evident in fuel tanks stretching to be positioned farther under the rider's seat, which has the added benefit of lessening the dynamic impact of a decreasing fuel load over race distance. Yamaha went as far as moving electrical components from their traditional spot in the front of the fairing to inside a frame rail or on top of the airbox, closer to the center of gravity. The engine, composing a large portion of the bike's weight, plays a large part in this aspect, but changing the engine's location is not a simple task. The relationship of the countershaft and swingarm pivot must be considered for the suspension's anti-squat characteristics. In the M1 presentation, Tsuji indicated that Yamaha is constantly refining the engine configuration in terms of the crankshaft and transmission layout, in order to optimize the center of gravity. The M1 has a jackshaft that allows the engine to spin backwards, which gives plenty of leeway for changes, and with the bike's machined crankcases a whole new layout is potentially just a few keystrokes and a pile of aluminum shavings away.
The fairings and tail sections of most of the MotoGP bikes have significantly slimmed down in the past couple of years, something that is counterintuitive to good aerodynamic design. For better speed and acceleration, a small frontal area and more-closed-in rear section are desired, but increased side areas lead to worse aerodynamics around the yaw axis. Imagine poking a stick vertically through the bike at roughly the gas cap and then spinning the bike around the stick. Just as better mass centralization would allow you to more easily spin the bike, a smaller side profile creates less wind resistance to this motion, likewise improving handling.
Increases in engine power have come hand-in-hand with improvements in ridability, both from changes to the engine itself and the addition of more electronic controls. The M1 press material indicates that power increased by 35 horsepower over the life of the 990cc M1, with a corresponding increase of 3000 rpm in maximum engine speed. Other manufacturers have shown similar strides in both numbers. While such increases in rpm surely come at the expense of a broad powerband, the electronics reduce that requirement with every iteration, allowing more freedom with aggressive camshafts, cylinder dimensions and so on.

This 360-degree crankshaft...

This 360-degree crankshaft (left) and camshaft (right) with identically timed lobes are from the original Twin Pulse Desmosedici, which had the two cylinders in each bank firing together. According to Filippo Preziosi, Ducati Corse's technical director, "The layout used from 2004 onwards was on the other hand similar to a twin but not entirely. In other words, combustion of the four cylinders was very close to 'two-by-two,' but not exactly at the same time as in 2002."

The RC211V crankshaft (left)...

The RC211V crankshaft (left) has its outer two throws (for the rear cylinders and two outer front cylinders) phased at 360 degrees, and these four cylinders fire as a standard V-4. The remaining cylinder is phased at 104.5 degrees and fires in between the close-firing pairs. In the RC211V firing-order chart above, the front bank of cylinders are numbers 1, 3 and 5, the rear bank, 2 and 4.

The '07 Honda RC212V sports...

The '07 Honda RC212V sports a tiny tail section and abbreviated fairing compared with the RC211V. This slimmer side area decreases yaw resistance, improving handling.
One of the first areas of concern when the class switched to four-stroke engines was the increased engine braking, which can be controlled to a certain extent with a slipper clutch. One early addition to the slipper clutch, used by both Honda and Yamaha, was an air bypass circuit in the induction system. By allowing air past the throttle plates on deceleration, engine braking is reduced, easing the load on the clutch itself-a similar setup is used on Honda's new CBR600RR. Furthermore, when the various versions of fly-by-wire throttle control were introduced over time, these could be used to hold the throttle open on deceleration, again lessening the work done by the clutch itself. Certainly controlling engine braking by electronics would be more accurate and consistent as the clutch and rear-tire wear, and even offers the opportunity for the rider to adjust engine braking on the track or a heuristic approach that adapts itself to the various conditions.
From those first electronic engine braking controls, the number of sensors and degree of engine management have blossomed to include traction, wheelie and launch controls in addition to taming the ever-increasing power output in the lower gears. Honda's technical-information bulletin for the '04 RC211V details the change to an "intelligent throttle-control system," in which the percentage of actual throttle-plate movement versus the percentage of twistgrip rotation varies from gear to gear. In first gear, maximum throttle from the rider's point of view equates to only 50 percent of maximum at the throttle bodies!
The original Yamaha had a 180-degree crankshaft and standard inline-four firing order, but in '04 the M1 was revised with a 90-degree crankshaft, which mimics the firing order of a 90-degree V-4. The M1's crankshaft spins opposite the wheels, with a jackshaft between it and the clutch that can be used as a counterbalancer, allowing more freedom to experiment with alternate layouts.
Another part of the ridability equation is found in the use of closer-order firing sequences for a big-bang effect. Both Yamaha and Kawasaki began in '02 with standard firing orders in their inline four-cylinder engines, but later switched to close-order formats, Yamaha in '04 and Kawasaki in '05. Ducati originally planned to have the Desmosedici set up in a "twin pulse" configuration, with the two cylinders in each bank of the V-4 firing at the same time, but this caused durability problems. Before '04 the company used a standard layout and then switched to an "asymmetrical twin-pulse" configuration. In a 2005 interview, Masao Furusawa, head of the M1 project, stated that the switch to a four-valve head from Yamaha's signature five-valve layout made a big improvement to ridability, and that the team is continually testing small differences in firing orders.
Over time the MotoGP bikes have sprouted more and more electronics to better control their potentially vicious power outputs. Every sensor on the M1 is paired with a spare in case of failure, adding to the complexity. Although many of the Yamaha's electronic components now reside on the top of the airbox or alongside a frame rail, the front of the bike is still loaded with gear.
One factor that has played an increasingly important role in MotoGP development is fuel consumption. Allowable fuel capacity steadily dropped from 24 liters in '02 to 22 liters in '06, but the reduction had little effect, as more electronic controls were utilized to steadily increase power and speed. Incredibly, for '07 it looks like even the drop in displacement hasn't fazed the top players in the class: The 800cc bikes are just as fast as the 990s were after five years of development, if not faster. How far they'll be along in another five years is anybody's guess.