That's just racing, there's no way to change it once the series is up and running. We discussed options a couple of months back for maintaining a level playing-field (look back through the DD threads) but the best suggestions need implementing before you issue a rule book.
You're right, it is galling when you're beaten by a machine that you know is quicker with a rider you know is slower, but you have to reflect on why you're racing - it's fine to walk away with the knowledge you're quicker. The only problem is when you're battling for the No1 spot (or a podium), then it can really get you down, but I was beaten into 4th twice this year (my second 4th at Assen......ARSE!) and both times I was beaten by better rider skills regardless of the bikes they were riding. Racing, like life, isn't perfect.... but it's better to be out playing than in watching.