Draft systems are like playoff systems. There's no single perfect way to do them because they're trying to balance multiple interests. Every time to tweak it to help one angle, people will say "but what about the other angle, that doesn't make sense" so they tweak it again, and it gets all weird and kludgy.
They have a lottery because while the general idea of tanking/rebuilding is fine, you want to avoid situations where teams have an extremely obvious, strong incentives to lose specific games you're selling tickets for. If there was no lottery, you'd have teams shooting into their own net by on opening night if there was a Gretzky level prospect.
Basically every change since then has been the result of something happening and a bunch of people saying "that feels unfair!" so they tweak the rules/percentages. They only draw for top two instead of top three because the Red Wings fell from 1st to 4th a few years ago and Yzerman pitched a fit. You can only move up a limited number of spots because the Flyers jumped from 13th to 2nd in 2017 and people said that felt unfair.