I've mentioned this on the Wii Fit Skype chat, but...
From my perspective, you ABSOLUTELY want to avoid Lylat Cruise at all costs. It's a really bad stage for us because of how the stage slants this way and that. If it's on an upwards slant, the stage just eats Sun Salutation unless you short hop it first. And if it's on a downwards slant, a lot of your physical attacking moves will just whiff completely against even medium sized characters. In addition, there's no way to reliably aim your Header shots if you're looking to perform a trick shot or bounce it on the floor from offstage because the uneven terrain sends the ball all over the place.
I know Anther's Ladder doesn't have this stagelist, but if you're playing with a larger stagelist that includes Halberd, Delfino, and Castle Siege and two bans, then your second ban should go to FD, SV, or Halberd depending on matchup. You would ban FD against characters who give Wii Fit trouble when trying to land (Diddy, Falcon, Sheik, etc.), Smashville against those characters who can use the platform to edgeguard Wii Fit where they couldn't before (Fox, King Dedede, etc.), and Halberd against Rosalina, Donkey Kong, Mii Brawler if he has access to Piston Punch, and small characters (Kirby, Mr. Game and Watch, etc.).
In general, Wii Fit wants to play on more platform-heavy stages, like Battlefield/Miiverse, Dreamland, and Town and City. Not only does it help supplement her landing game when she gets knocked into the air, but it also allows her to escape characters with high pressure options more effectively. She also gains the ability to pressure opponents on the platforms with high damage options. If you catch their landing on a platform at the right time, or if you can correctly read a tech/missed tech wakeup on a platform, you can score some high damage Nair combos. If they're shielding, you can use Header and take away about 30 of their 50 shield health to really lay on the pressure. In addition, Wii Fit's Usmash can hit opponents through the Battlefield and Dreamland platforms, after its recent hitbox buff. Very nice stuff, overall.
So these would be my habits when deciding on stages in a tournament set:
Striking w/ 3 Starters: Strike FD or SV depending on matchup.
Striking w/ 5 Starters feat. Dreamland: Strike FD and SV.
Striking w/ 5 Starters feat. Lylat Cruise: Strike Lylat, then FD or SV depending on matchup.
Banning on a Small Stagelist w/ 1 Ban: Ban Lylat.
Banning on a Large Stagelist w/ 2 Bans: Ban Lylat, then FD, SV, or Halberd depending on matchup.
Counterpicking on a Small Stagelist w/ 1 Ban: In order of priority, Battlefield/Miiverse, Dreamland, then Town and City.
Counterpicking on a Large Stagelist w/ 2 Bans: In order of priority, Battlefield/Miiverse, Dreamland, then Town and City.