What's wrong with that? That happens anyway in our current group structure? Surely you can say it's equal unfair for Nigeria to be stuck in a group with Iceland, Croatia and Argentina whilst Senegal are in a group with Japan, Colombia and Poland. I know what group I'd rather be in.
Or let's say you've got a group like this:
Rank the 6 teams into 3 groups of 2 based on their FIFA rankings, and make sure everyone plays one game against one of the ranks.
Who has the easiest set of games? Presumably one of the teams that don't have to play Brazil... but it's not exactly clear. Bolivia are the unlucky lowest rank team who have drawn Brazil, but they've also got Japan and Morocco. They need only 3-4 points to get into the top 4 and into the knockout round.
And anyone who can't get 3 points from those games doesn't deserve to go through.
The most unfair thing is that you can win all three games and still come second. Ie. if Wales beat Switzerland, Japan and Morocco 1-0, whilst Brazil beat Switzerland, Japan and Bolivia 2-0, then yes, Wales have won all three games but still come second. But actually, the played two of the same teams, and Brazil beat them by more goals