Use Homing and Super Missiles. Surprise them with a Charge Shot. Or, fire a Super Missile with a Charge Shot. They'll have to block instead, and a slight lag will not allow them to use the PSI Magnet in time.
Apply the same with G&W. If you want, fill up his bucket, because once that is out of the way, he cannot absorb anymore of Samus' Charge Shot. All you'll have to do is stay out of the way, which should be easy with a few Homing Missiles and z-airs.
Projectiles are used further away from the enemy, and it isn't like Peach will always be using Toad in her defense, lest she mistaken an attack and gets grabbed instead. It has a nice lag if not used properly. Toad can only block one projectile at a time, which means Super Missile + Charge Shot = 25% damage.
Pit has a slight lag in putting up his Mirror Shield. The same is applied for putting it away. Simply surprising Pit or having him think you're going to use a Charge Shot helps, especially if you use the Charge Shot the moment he isn't expecting it.
In these battles, I use Homing/Super Missiles and Charge Shots when my opponent is least expecting it. You just need to know who you're going against.
Nayru's Love is short, but can be used immediately after. However, you can trick your opponent by firing a Super Missile, and then a Charge Shot. When Samus' Charge Shot is fully charged, it will eat through Super Missiles and continue flying toward the opponent, which means that if Zelda isn't expecting the Charge Shot to fly at her, she's left open.
These are just the ones I can think of off the top of my head. The presence of these characters make it a risky gamble to use a skill that would otherwise be a pocket ace for Samus to use when you need it most.
In the end, U, D, U, D, U, D, U, D works too. That is, if you are good at transforming into Zero Suit Samus. If not, simply hold the right side of the D-pad down and the toggle up and down at a fast pace to shed that lovely armor.