Interestingly, unlike you that your LI was Vega and you used him as a companion in battle as well, my Shepard's LI was Ashley, but she had an annoying AI bug that made her unplayable for me, so I rarely used her.
That sh*t was introduced with a patch and happens when you skill Marksman - which just so happens to be her signature skill. Best solution is to turn auto skill usage off, she'll fight just like normal then.
Used to think I'd be annoyed by it, but I now prefer to always have their skills ready when I need them. It's not like the "let them be themselves"-approach is very efficient anyways, since party members without orders only deal 50% weapon damage. Ash with a Lancer X & Marksman is a fine ruiner of sh*t, though.
I always had Ash in my group, sadly she's only available for about half of the trilogy on total. Not only for, uh, obvious reasons, but also since she fights exactly like Zaeed, my bro from ME2. He's an okay surrogate, yet less pleasant to look at, though.