The problem is, people think back to the old gp500 days with a very misplaced sense of nostalgia. I think this comes in part because the era gets remembered not so much by what it really was like, but by how you experience it today by watching youtube clips. Which youtube video's do you think get watched the most? Those with exceptionally exiting races. They conveniently forget that these were the exceptions rather than the norm. And of course a 5 minute race review is more action packed than watching a full race. So you get a very distorted picture of big grids at the start (failing to see just how wide the distribution in lap times was, in other words, how slow the back-markers were relative to the mid-pack and the mid-pack relative to the front runners) and exiting racing right until the chequered flag (ignoring the many races with dominating victories).
Truth is, gp racing has been between a very select number of factory backed honda and yamaha riders most of the time, with never more than 3, maybe 4 really competitive riders on those bikes.
I absolutely agree with you, this is in the nature of prototype racing. If you want to see a more equalized grid, watch sbk. Be glad that that option is available, rather than moan about how gp should become more like sbk.