I don't think it really matters either way... I mean, try to give Sakurai some credit on the issues, here. Until we see or hear otherwise, I don't think it's unreasonable to expect that the Final Smashes with a tighter focus area will do more damage than those with the capability to hit up to an entire screen's worth of characters.
All characters being able to be hit during a Final Smash, not just Link, could be just as beneficial to gameplay as it could harmful. In one-on-ones, as mentioned, it's not really going to matter. A Final Smash is probably a guaranteed death for your opponents. In multi-player battles though, being stationary and vulnerable while performing a Final Smash might actually require you to *gasp* incorperate timing and strategy into your attack plan.
Oh, Samus is going to use her Zero Laser on the two opponents to the right of her? That's great, I'm on her left. Times to charge up Bowser's headbutt as high as it'll go and punish the crap out of her.