The problem is polarization. If all of her moves are projectiles, then characters with reflectors will have too much power over her. Fox and Ness could hole up in their Reflector and PSI Shield respectively, and she wouldn't be able to do much about it. If Hero gets bounce, she's completely invalidated. On the other side, if a character can't deal with projectiles, she just wins.
Mega Man already has this issue to some extent with just the Mega Buster, if Samus were to trade all of her normal attacks for her projectile weapon, then it would become a big problem.
There is also some logic in the melee strikes, albeit mostly for game design reasons. Samus's projectiles (aside from a charged Charge Shot) are fairly terrible options up close, as they're either unsafe on hit, or too slow to expect to not get punished for using them. This is even more true in the Metroid series since hitstun isn't really a thing for Samus's enemies. Previously, your only option was to run away, but they introduced the Melee Counter so you can have a quick "get off me" option that stops attacks in their tracks and gets you some free hits in by decking them in the face, which I personally think fits Samus more since she kind of leans into the action hero tropes. With the new Dash Melee Counter, she can just bum rush things to stun and take them out before they get a chance to do anything, which is just cool.