I'm at the part where we get Sekune in our party, and honestly unlike the grandpa, she's absolutely useless. I equipped her with a weapon and even used the box select to select everyone. Why does she not have her own AI. I have to click at enemy's just for her to do anything, and she feels like a burden that makes the game annoyingly difficult. Is there any way to actually manage her better, or a pause function similar to infinity engine games? Or do I have to wildly swing everywhere and occasionally click to get her to kill someone?

If there are any more party members that I'm going to have to manage them this way, I'm definitely gonna break a mouse/keyboard or two.

Well yeah there is a way. You can choose your whole team when you hold your left key of your mouse and select all people. If it's right you should see 2 blue circle around your characters and one green circle for the character you are actually using that the moment. With TAB you can switch through your characters, but when all are selected they automatically attack the one you click with your right mouse button and pressing CTRL at the same time.

Even with AI she is pretty useless. She usually unloads all ranged weapon ammo onto the weakest mob, usually wasting more than half of it. There is a way to set how many times she should fire, but too much trouble. The manual has good tips on how to control your party.