Why should you get more points because you win in 125cc? That's b.s., too. Why aren't AMA and BSB and WSBK championships counted? They are harder than the opening support class, in my opinion.
I've read (before my time, so I don't know) that the smaller GP classes were regarded in similar importance to the premier class. Guys would race both 500s and 250s at the same Grand Prix, and try to win both championships in the same year. Ago, for example, won dual championships every year from 1968-72. So they should be counted to be fair to the old-school crew, though maybe not fully as important as the premier class.
In my mind, a championship is a championship, doesn't matter if you won by a single point or wiped the floor with the field all season long. Titles are of utmost importance. Then, add in winning percentage or races won (normalized for number of races in a season) in non-championship years - that is, if you didn't win the title, were you consistently competitive, or absent? - but races won should not count as much as titles won. Definitely should not count as several times the importance, as in the above chart.