This problem was put to a British University 5 years ago, in order to find a formula that would allow the 4s to compete with the twins fairly.
Titomike it was not the Flamini that decided the rules originally
The rules existed from the beginning, it was a small window left by the rules to invite other manufacturrs. There was no Ducati to compete then really! The RC30 ruled WSB back then.
But Ducati saw this and as they were able to put their act together, they built the 888 superbike and got their first championship! Raymond Roche was the Ducati rider that used the potential first. Until 5 years ago the twins also had a 15 kg weight advantage over the 4s! Things had to change as the Ducati (no other twin existed) was getting better and better.
After that the balance started changing and the twins got to level weight with the 4s, they had to use lead inserts many times during rules changing.
Remember that Ducati only used the full capacity allowed (1000 cc) in the last two years, they could still win with less cc before that!
Even Honda had to revert to a V twin to win again. The RC45 only got one championship and that was with Kocinski, after a lot of money was spent.
The main problem now is that although the 4s have about the same power with the twins, and sometimes even better top speeds, they lack a lot in acceleration out of the corners as they have a much better midrange power than the 4s.
This translates in easy overtaking at the end of the straight that folow any curve