I think some people are confused about the seeding for Wimbledon.
I don't know the full details, but I'll attempt to explain. The formula for Wimbledon has been the same for some time and Federer being the first seed was always going to happen.
For the men's side they take into account the the past two years performances on grass and amplify them, hence why Federer leaps Nadal (the gap is small anyway). The reason why they do it is because the ATP rankings don't really take into account grasscourt events. The season is short, therefore the ATP rankings don't reflect performances on the surface accurately unlike clay where there are 3 masters 1000 titles before RG. Hard courts are played most of the year, so again no need for adjustment.
So the rankings are not based on player prestige at all.
On the Serena debate, I'm less knowledgable on it, but it does open the debate for protected rankings for those on maternity leave. Maybe it's not consistent with what's happened in the past, but if one can consider it progression, maybe it's not an issue.