They don't so much restrict certain manufacturers as they do the type of machine. When Aprillia and Honda were in WSB with their twins they were subject to the same rules as the Ducati, I believe they had a weight penalty of 15 pounds over four cylinders. Of course it has been shown that a 1000cc twin makes as much or more horsepower as a 750cc four. But lately the twins are putting up more power than the 750's could muster, and the twin won't spin the rear tire as much which makes it easier to get on the throttle easier. This is because with a twin the first cylinder fires and then 90 degrees later the second cylinder fires, then you get 270 degrees of rotation before the first cylinder fires again. This allows the tire to regain traction. Where as a four has a cylinder firing every 90 degrees. So there are distinct differences. With a 1000cc four you still have some of the same traction problems making it a little more difficult to ride, but you get a lot more horsepower and you have a wider powerband than with a 750. Now all machines have the same minimum weight but they have some restrictions on the four's to make it interesting. I imagine they will be a little more lenient on the fours next year in WSB as they homologate the rules with the AMA as well. The reason they need to add restrictions are that the bikes are production based. They have to keep many of the stock parts, this is to keep costs down, so the teams aren't allowed to use special valve heads or recast engine blocks to flow better.
Also a twin turns easier I think because of the engine layout and moments of inertia that I remember being explained somewhere but I don't remember the details. So you get a twin that may handle better and a four that has more horsepower.
This isn't like Nascar where they give Ford or Dodge a break to make them competitive. Which I feel is retarded. But they all have the same layout, front engined V-8s.
You can't split the classes out into fours and twins, you would have an all Ducati series(since Aprillia doesn't race the Mille anymore, and Honda didn't field an RC51 WSB team this year and is dropping the RC51 in AMA for the new CBR). Then you would have a class of all four cylinder machines which isn't as interesting as watching a twin battle a four. Then you have to think of viewership, if Ducatis aren't your thing then you will watch the Japanese bikes race and vice versa. By combining the classes you get a larger market for one series.
It looks like Ducati is going to pour some money into the AMA next year since it is rumored that Ruben Xaus(currently on the Ducati WSB main team) will be switching to the AMA. Which should be good for AMA racing, the more factory teams the better.
Now in MotoGP I believe the bikes are wide open(which they should be since they are not based on production machines and homologation like in Superbike racing). But they do have weight limitations depending on the number of cylinders. A twin has the lightest weight limit, followed by triples and so on. Which is great since you see all sorts of configurations. You get an inline 3 from Aprillia, an inline 4 from Kawasaki, a V-4 from Ducati, a V-5 from Honda(and a rumored V-6 possibly next year) which makes it very interesting. Since it is wide open the companies can make changes to their machines to make them competitive.
Sorry for the long post, I don't get to talk racing with anyone I know since I am the only into it.
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That Champion Valentino might think so anyway... 
