I wouldn't say there's more bosses, but there are more enemies..
Let's just check:
MP1:
Flaaghra
Thardus
Omega Pirate
Meta Ridley
Metroid Prime
MP2:
Amorbis
Chykka
Quadraxis
Dark Samus
Emperor Ing
So there's the same number in each game, BUT MP2 has multiple forms of each boss (Amorbis 1-2, Chykka 1-3, Quadraxis 1-3, Dark Samus 1-4, Emperor Ing 1-3) making them harder to beat AND just like MP1, you lose most of your weaponry again in MP2 and you have to fight Guardians to get them back (much harder than MP1)!
Don't forget, there's more weapons and advancements to obtain in MP2 as well (Seeker Missile, Screw Attack, Boost Ball Jump, Wall Jump, Dark Beam, Light Beam...)!
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