I feel like it's much better to give a character more diversity than strictly keeping to the lore and thus limiting your options. I love the MOTHER games, and I don't feel like giving Ness/Lucas moves or items they don't use in their respective games is all that bad. I feel like giving the rope snake to Lucas, for instance, was a great way to differentiate him a lot more from Ness, and make him more unique as a character, given that there's only so many characters with a tether recovery option.
Especially given these characters come from a series with highly stylized graphics for their special abilities (where they just are weird symbol patterns that move across the screen). So what if Ness/Lucas never use PK Starstorm or PK Thunder in their respective games? It make much more sense from a gameplay standpoint than PSI Rockin (or PK Love). PK Starstorm actually takes form as something you can visualize, and also has the "magnitude" to be a final smash.
PK Thunder is in the same boat. A lightning jolt is much easier to visualize than a... wave of psychic power I guess? Plus it has given Ness and Lucas the opportunity to become incredibly unique from a gameplay standpoint; there's no other character in the series who has a recovery mechanic as original as PK Thunder.