Alya was about 10 levels behind the rest of my party when I got her... I had found the perfect spot to powerlevel everyone in Kasmir's castle: the three sleeping henches that instantly respawn when you step out of the room. One casting of Ice Water from Frog and Marle kills them all in one shot, even at relatively low levels. Tapping the speed-up-emulation key at exactly the right times shaved off about 80% of the time I would have otherwise had to spend walking the characters back and forth, waiting for their turns to come up in battle, or waiting for the characters to finish their victory poses. I just gave one of them a silver stud and supplemented ethers and aura heals out of battle as needed, then went to town.
Another excellent powerleveling spot I found later after I got Alya was the second to last room in the ocean palace (the real ocean palace, not the ruins) where three of those elemental bat/cyclops creatures appear. For some reason, Magus' Double Tap attack does ridiculous amounts of damage to them (like around 3000 damage per hit... way more than his regular attack value). A few other monsters were weak to it too, but not all, and the three little guys grant a lot of XP. I'm not sure if it had to do with any equipment Magus was wearing or what, but it didn't seem I was using anything out of the ordinary.