I know this is more of a pet peeve than anything else, but the current way things such as prefix are setup as well as weight, etc are all clustered together under "perms" instead of somewhere that's easier and nicer to read.

Example:

Pex has it as such:

permissions:
    - '*'
    - permissions.*
inheritance:
    - Moderator
options:
    default: false
    prefix: '&3&lOWNER&r '
    suffix: '&3&lTEST&r '
worlds:
    World_Nether:
        permissions:
            - test.permissions1
            - test.permissions2
            - test.permissions3

How Luck has it set:

name: owner
perms:
    global-world_nether/group.moderator: true
    'prefix.0.&3&lOWNER&r ': true
    permissions.*: true
    'suffix.0.&3&lTEST&r ': true
    group.moderator: true
    '*': true

It would be nice if we could have a better formatted flat file instead of the "cramped" system there is now. Would make reading through everything much easier too among other things. If there is any specific reason why it is formatted the way it is as of now, I would like to know why, and if there is any possibility for it to get a "better looking" format.

They're stored internally this way too.

I plan to make it so that the output is sorted, but a complete redesign probably wouldn't make sense / be easily possible.

How does the formatting looks like now? Before I change to this plugin I would like to know it :)

It's alphabetically sorted.

I find the flatfile very weird looking to be honest... Is it going to be changed?

Bumping this issue to bring attention to this commit.
85c7a7d

The improvements you suggested were implemented in the latest version. :)