It would be nice to have a playerSetGroup to change the player's group, instead of just adding the group. Some permissions plugins don't make an added group the default group (no prefixes, etc) and this would.

As i said, there's only 1-2 plugins that support default groups. All other permission plugins do not use any form of defaults, or 'primary'. Other plugins use Weights, which are numerical representations and whichever has highest or lowest is default. Because there is no standard way to perform what you're requesting I can't put in functionality that would be easily functional between more than a couple permission systems.

Most permissions plugins don't have 'default groups' So these plugins which handle group resolution based on primary (or default)/secondary groups are in the minority. Vault is a generic plugin API, if someone is wanting specific methods such as setting a group default they should probably be linking directly into your permission plugin.

In that case I would have to link directly into each permission plugin I want to support, minus a couple.

I looked into it more, and you are wrong.
The following plugins, perhaps more, support what I am looking for and provide ways to do so:

PermissionsBukkit
GroupManager
DroxPerms
bPermissions
zPermissions
PermissionsEx

I'd really appreciate it if you would add this feature.

@Sleaker I think he think's about replacing all present groups with one new. Then the weights, default groups and so on are not important, right @koalaaaa?

Correct, @criztovyl. using playerSetGroup would remove all existing groups and add the one specified. The plugins I listed above support that, and I'm sure the rest do.

@koalaaaa - Vault is open source and accepts Pull requests, if you feel it's something you need please feel free to take the time and add it in.