Obligatory: FFT's allowing recruitment of Orlandu/TG Cid?
To be honest, Orlandu isn't as game-breakingly powerful if you take away his Excalibur. Typically, I gave all the best Knight Swords to everyone else before him, since he can be plenty effective with just a Defender.
A more difficult problem is Calculator skills. They break the game pretty badly if you use them as Secondary, instead of being the slow, low-MA Calculator. Eventually I just stopped using them altogether, as the search for a good calculate result just took too damn long. They might've been more balanced if you couldn't see what stuff a calculate would target before executing the skill. That way you would have to either manually look at all the numbers yourself, or just wing it. That, or less Math Skill options. Taking out CT and/or 5 would do wonders, as then you couldn't just cast something with CT-5 to hit most of the units on the field.