All right, it's official: Snape/Flitwick is now one of my favorite pairings. I'd never even thought of this couple before the hp_beholder fest, and now, after two superb stories, I'm sold. You've taken the bare bones present in canon and added sinew, blood, and soul to create a complex and layered Filius who's a joy to read about. His story is so full and multi-dimensional. The charm-gone-bad-Azkaban backstory (with Xenophilius as his partner-in-crime!) makes such character sense, and then it turns out to make such clever plot sense, too -- very nice. (And the performing-cherry party trick -- hilarious.) Your version of the battle scene is wonderful -- I love when good stories fit perfectly into canon.
I find Snape's psychological progression very believable, too.
At the risk of annoying you by simply quoting your story back at you, I'm going to offer a few of my favorite lines -- so evocative and revealing.
Such self-delusions had been ripped like flesh from bone at the loss of Lily that moth-like tendency to the powerful, continuing until he was badly burned, or until the light itself went out thinking he would be enthusiastic about their particular variety of contemporary noise just because he wore black and washed his hair slightly less often than most "I'm sure that using wildlife is against the rules," Severus grumbled from his breathless, cakeless position on Filius' carpet. it had eaten up his heart piece by piece until there had probably been nothing left to give even if she had decided she wanted it This was probably the worst way to ask someone to commence intimate relations since Elgin the Elder sent a singing love letter by troll-post Like a fountain that was once completely dry but had since been filled with bright water
And as a lovely bonus, I also got to learn the not-a-word-of-it-a-lie, totally true story of wizard Mozart. I knew he didn't die. I knew it.
Plus, I think your version of Albus is spot-on: always calculating, always unreadable, often necessary.
One grammar point: you don't need apostrophes with possessive "its" (as in this line [and several others]: cat winding about it's owner's legs, or a snake appraising it's next meal)