It's better to focus going deeper into a few skills in terms of overall level at the moment. Previously it was better to spread it around but now it's definitely better to stacks skill points AND stats into a few skills since the amount of skill experience you learn at the higher levels will allow you to get to a much higher level over time.
You can get a ton of levels out of maxing stewardship, leadership, and charm and you can use those levels to put enough points into a single weapon proficiency to then get some levels out of that. Once you get your pts invested into your core skill you will have some extra levels to spend on other skills that you would want but you are much better off focusing on a few skills at first.
This also makes companions that start with a skill high and MAXED (red) a poor investment. Choose companions that have room to grow into their specialty (blacksmith, scout, medicine, engineer) since they will end up with more flexibility in the long run.