Assault Rifle excels at boss fighting, while Launcher will be better for pretty much everything else.
For bosses, Blight Rounds are invaluable, and Rifle also has a few PAs that can do several hits of massive damage to a single target, such as Positron Blast or Satellite Cannon.
Launcher does typically have a stronger normal attack, and is able to deal large damage to an area quickly and easily, but it will fall short of effective use of a Rifle in boss fights. While some PAs do have multiple hits, they tend to be a bit weaker and less accurate.
Plus, with Launchers, to my knowledge all of its PAs will only affect one part, unless you manually move during Flame Round or get Nova Blast in a weird spot. Rifle however has a few PAs, such as the aforementioned Positron Blast, that deal their damage with a piercing projectile, allowing multiple parts to be hit along their path, and preventing being blocked in most cases. This is useful on nearly all bosses, but in certain cases, such as Bar Lodos, it can be particularly devastating with careful aim.
That said, it does take a good deal more practice and management to use a Rifle effectively than a Launcher, so if you prefer the simplicity of Launcher combat, stick with that rather than forcing yourself to use a Rifle just to be optimal.