Kind of an interesting note, since most of the world revisits in KH2 involve the Heartless, the Disney villain fights are somewhat overshadowed, though they are also evenly distributed between the Heartless, and the Nobodies.
This is probably why KH3 feels more jarring if you come directly from KH2, since the plot structure requires all major boss fights to be at the end, whereas in KH2 Org. 13 is further built up than in CoM.
Granted, KH2 also has more factions that are important than in KH3. In KH2 you have Hades, Maleficent & Pete, Org. members, independent Villains, and the pseudo-antagonist status of Ansem the Wise & Riku in disguise. In KH3 you have independent Villains, Hades, and Org. members, since Maleficent & Pete only set up future events, and the secret hidden faction of Foretellers don't show up until after the end.
Most of interesting stuff in KH3 happens either in Org.'s structure (Vexen & Demyx doing the replica stuff, Saix in the reports, Luxord's attempts at figuring out Xigbar, Ansem SoD's search for Subject X, Xemnas attempting to re-do Days/DDD etc.), or is caused by lack of coordination between Guardians until the end.
This wouldn't matter much if the final fight was a proper conclusion to some of main characters' arcs, but outside of Xion, and maybe Roxas & Naminé, you don't get that either. Ventus has the whole Dandelion stuff, Twilight Town folks have the Subject X, Donald & Goofy have their own Keyblades to look forward to, SRK are divided again, most of the Org. members have their own plotlines to cover etc.
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The MacGuffins of the series probably also deserve some mention:
**In KH1, the big MacGuffin was The Door to Darkness (a Kanji pun, since the Kanji for Yami contains the shape of a gate, which is also the Kanji for door), which required Final Keyhole to be opened, which required all other Keyholes to be opened, and Princesses of Light to be gathered. Rather complicated, but essentially Ansem SoD wanted to brute force himself to the depths of Realm of Darkness to find Kingdom Hearts. He does, and it destroys him.
He of course doesn't realise this KH is technically a false one.
**In CoM, the MacGuffins are the main trio of SRN. Marluxia desires Sora to become his puppet, Riku is desired by Vexen & Ansem SoD's remnant, and Naminé is needed to manipulate them both.
**In KH2, Kingdom Hearts is still the main MacGuffin, but the approach is different, rather going to where KH is, Xemnas gathers hearts to create an artificial one to absorb the real one's power, though he assumes he is beckoning the real one.
In this mode, destroying worlds becomes meaningless, since they harbor valuable hearts than can weave together the Kingdom Hearts. So the goal becomes causing trouble to artificially expand Heartless just enough to make this possible, but not too much to blow up worlds.
Then we move to the other games:
**In Coded, the MacGuffin is Book of Prophecies, which we later find out can become its own data realm like Jiminy's Journal, which is the setting of most of the game.
**In Days, Xion herself is the main MacGuffin, though Days still has unanswered questions.
**In BBS, the MacGuffin is the x-blade, which can manipulate the real Kingdom Hearts without needing another artificial one.
**In Days, the MacGuffin is Sora himself again, who ends up failing the exam, thus retroactively making himself less valuable.
**In KH3, x-blade returns, the real, complete one this time, and becomes in theory the second default Keyblade of Sora. The secondary MacGuffin of the black box from Back Cover is reintroduced here, and though it is relevant to MoM's plan, it is irrelevant to the broader lore of the series, and most of the game.