I am promoting rookies to Low A and Low A to High A and so on. Do you have to do them individually or is there some shortcut I am missing out on?

Individual. With advanced roster mode, you can select multiple players and promote with one click.

Once you've completed 3 seasons you can use Advanced Mode (this can be found at the bottom of the Management Console, which is an option under the Manager menu tab), which enables you to perform multiple transactions at once, as frymaster said, but until then you'll have to do them individually.

Why do they make you wait 3 seasons? Never mind I just remembered this is WIS and lots of stuff makes no sense!

The idea is to prevent new owners from making mass stupid mistakes. But, truth is, it makes a complicated, time-consuming game more time consuming for people who are deciding if they'd like to keep playing.

And probably makes mistakes more likely, not less, with frustrated players rushing through something. Making someone click through an "Are you sure" step is great until it's been done about 10 times, after which they know where to click next and do it without slowing down to look at anything. It makes sense for about the first 30 days a new owner is playing. After that it's counterproductive.

Looks like they're listening... maybe...

Now all we need are rookie owners.

Within 24 hours someone will say "I'm new and I accidentally released 9 BL players. Will WifS undo this for me? If they don't, I'm done with this game!!!!"