I have two level 25 pets yet when I click on the proficiency tree, the 5 point attacks are still gray...

Have you spent any proficiency points yet? If i'm not wrong, you need to use 5 points to unlock the 5 point attacks and so forth.

If you haven't used any level up/proficiency points, I would really recommend you to read this guide: https://www.sylestia.com/forums/?thread=11101
It gives advice on how to use the points as well as equip your pets so that they are more effective in battle.

The main tip is to choose between intelligence OR strength for each pet. Between the two, only one can be used. So if you choose strength, don't add any points in intelligence, and vice versa. Likewise, choose a proficiency tree that matches the stat you've picked. And when equipping, choose equipment that adds more to the main stat you've picked. Don't use equipment that adds more to the other stat, or split points equally.

I have a pet at level 40 and have saved 2 proficiency points for enhanced beam because it says it costs 2 points. I have one point into improved beam, but enhanced beam still is grayed out and I can't put the points into it. Do I have to fill improved beam all the way with 5 points before enhanced beam becomes available?

Link: https://www.sylestia.com/forums/?thread=27702&page=1#3 Author: MsStarshine Time Posted: 10/13/2015 at 7:01 PM I have a pet at level 40 and have saved 2 proficiency points for enhanced beam because it says it costs 2 points. I have one point into improved beam, but enhanced beam still is grayed out and I can't put the points into it. Do I have to fill improved beam all the way with 5 points before enhanced beam becomes available?

Correct. So your pets have to be at least lvl 60 before you can get enhanced beam.