Reading through the thread, I've seen a few complaints about the skill system. I agree, it's a pain in the ass. After spending way too much time trying to allocate certain skills I've learned a very important lesson that I want to share with everyone that is just starting: it's mostly not worth it.
It's easy to be confused or obsess about the skill system. Here is a guide to make the experience as painless as possible:
Step 1: Get that first column
Try to fill up the first column (vertical). It gives you +20 to all stats. That's amazing in the early game. Don't worry about stacking skills or horizontal lines. Just focus on getting that first column on as many characters as possible. Stacks and horizontal lines aren't worth it until you can get a ton of them, which isn't possible in the first half of the game.
Step 2: Learning to let go
At some point, probably once you leave Hyland and go to a different empire, you will have gear that is 3-4 tiers better than your current gear. Equip it all, give no fucks about the skills. It's hard to sacrifice that first column you worked on, but the new gear will easily compensate for it. Believe me, I had the first three columns completely filled up with Edna, but equipping new gear that gave me nothing was still better.
Step 3: Abusing Armitization
Slowly start working on getting the 5th column filled up on your two human characters. Nothing else matters. That column will give you massive boosts to your BG meter. As we all know Armitization is OP. With that column filled up you pretty much will always have it at your disposal. The seraphs can just equip their best gear in terms of stats, don't worry about skills.
This should hold you up for a big chunk of the game.