2.0.3 saves are compatible with 2.0, yeah. I've made some changes to what abilities certain GFs start with and Cerberus' Compatibility value that won't be reflected when playing off of a 2.0 save, but everything else will work like it's supposed to. As far as the Aberrant monsters go, I assume you're referring to the five involved in that sidequest. These are the ones that can heal themselves:
Ruby Dragon: Hit it with Ice- and Water-element attacks regularly to slow the rate at which it heals. Magic, Elem-Atk-J, Shiva, and Leviathan all work. Jelleyes in Centra, when encountered alone, are an easy source of Blizzaga spells, and they have Blizzara when encountered in duos. You can also Blind, Poison, and Slow it; Slow in particular is good here since the boss' healing happens when it gets its turn. Poison is harder to inflict, but deals a lot of damage. In addition to ST-Atk-J and the spells that inflict these effects, Shiva inflicts Slow and Leviathan inflicts Blind. Bad Breath, Dark Shot, and Doomtrain can inflict all three at once.
Malboro: It's weak to Fire. If its White Wind is a problem, you can zombify it.
Abyss Worm: Vampire is a physical attack, so anything that mitigates physical damage will lessen how much it heals. Characters with high Speed also have a chance to dodge it, and you can inflict it with Blind too.
I've also increased some characters', GFs', and weapons' stats since 2.0, as well as the usefulness of abilities like MiniMog, so you may find these a bit easier after updating based on that alone.
