Forgot about Alastor; before I knew about the PSA that can be found on the
boards/vault, I would never have included him. But after looking at the move set it just clicked with me. While you can say he's more akin to Ganondorf or Captain Falcon, he has this charge mechanic for his neutral B. You can still pull of the scythe spin if you do a Turnaround Neutral B, but if you keep that charge, your Neutral, Side, or Aerial Up B get powered up. Symbolically for Project M, an original character would help keep that "grassroots" feel that Project M kind of embraces now... (I also liked the character concept so much that I made new cosmetic assets for the character.)
As for ordering, I kept the most recognizable characters from their series in front, then I looked at Ondo's Out Of The Box CSS layout and the organization from Smash 4, Project M and "picked 'n chose" what felt right. I can't explain it, but to me personally it worked.
If I tried to make a 4-row variant, I might still be working on it...
Edit: Andross I always felt needed to be fighting along side wolf, and there's a moveset concept I found on deviant art that pulled me over. Think of Marvel Vs. Capcom's (or any figihting game with Magneto in it) Magneto play style and you have the core inspiration for an Andross moveset. Plus I always think Smash Bros could use more villains. But if there's no Andross PSA ever being made, I'd consider Slippy going before wolf unless Krystal somehow get's a PSA made.
TL:DR I look for characters that can add something new to Brawl/Project M; Alastor puts a unique twist on the FalconDorf Formula, others like Waluigi and the other Villains all bring something new thanks to their origins while also feeling at home if they ever were in Smash Bros officially. Plus Tabuu has a unique play style that revolves around spacing and patience (if you use the PSA on the vault). Placement of the single series reps go in line with either PM, Ondo's out of the Box CSS, or those that have the best thematic matching... this explains Pit with the Fire Emblem Series.
Edit 2: Made a 4 row variant that includes Knuckle Joe:
Note: There's only 3 more I can see myself adding to this: Top Row gets Lord Frederick from Tropical Freeze, Second Row gets Slippy, Third Row gets Raichu since Pichu is now Brawl Pikachu, and the Last row gets a Second Random slot to homage Melee's CSS (and both Random Slots may be invisible now).