First of all, I really like that you a) included more stages and b) decided to include PW4's feature of separating the bigger arcs into several stages/sections to give them more breathing room. That said, if you include more locations, you necessarily also have to fill them with content and characters to fight, so you will imo need more NPC's than you included in your list. I'll go through them stage by stage:
Shell Town
Morgan is more than enough for this little arc 
Orange Town
If you keep Alvida as Buggy's henchmen for this arc, that's enough
Syrup Village
Since I would make Kuro a playable character, no NPCs for this arc. And I don't think any would be necessary either.
Baratie
I guess one could discuss making Gin into an NPC, but I don't think it's really needed, since Mihawk is also around as someone to fight. Since Krieg would be playable in my version, no NPC's.
Arlong Park
Arlong would be playable in my version and Hachi is more than enough as an NPC.
Loguetown
Nothing really to add to this stage, either.
Whiskey Peak
I think Whiskey Peak would make a great stage, since even in the manga, it basically revolves around fighting a large number of enemies. But as puffing.cinema pointed out, you would really need Mr. 5 and Miss Valentine as NPCs to make it work. Since you can then go and also include them in Little Garden, this all works out.
Little Garden
With Mr. 3, Mr. 5 and Miss Valentine, you have more than enough villain NPCs. Give them a big army of henchmen and this can work well as a stage (I guess you could include random dinosaurs as NPCs as well...). I don't think you really need Brogy and Dory - you can jsut have them in a cut scene and then simply be part of the scenery afterwards.
Drum Island
Wapol's henchmen aren't worthy of being NPCs. I guess one could include Dalton as a supporting NPC, but since nah, the Lapahns are enough.
Alabasta+
Agree with separating it into two stages - how did PW4 separate it? Was the first part Nanohana or was it Rainbase (or both)?
I've never seen this one suggested anywhere, I think, but imo Miss Doublefinger would make a good NPC. She had cool powers and a neat design, and her fight against was Nami was pretty good. I also thought about Miss Merry Christmas and Mr. Four simply to include that great Usopp moment in the game, but I have a really hard time imagining them as NPCs xD.
Jaya
Not much to say about this one. Bellamy is still an NPC in my version and that's enough.
Skypiea+
Now I don't disagree with turning Skypiea into two stages, but then you really need more characters for this arc than just Wyper and Enel. As another supporting NPC, I could see Gan Fall. And even though barely anybody cares about them, you'd really need to include some of the priests. Ohm and Gedatsu would be the obvious choices for NPCs, but there could be a case made for Satori (hohoho!)
Long Ring Long Island
I'm very unsure if this arc would work well as a stage in a Pirate Warriors game. It doesn't really suitthe usual "a giant hord of enemies are swarming you" gameplay. If it wasn't included, that would also remove Foxy as an NPC.
Water 7+
I'm not sure, if this one really needs to be two stages, but I guess the first could focus on all the trouble with the Franky family and the second stage on the fight against CP9.
As NPCs for both Water 7 and Enies Lobby, I'd include Paulie and Kalifa.
Puffing Tom
Another one where I'm not sure if that really needs to be a stage. I don't really want Nero, Wanze etc. as NPCs either 
Enies Lobby
Well, as I said, I'd include Kalifa among the villains as an NPC. While I personally would love to include all of the CP9, adding Kumadori and Fukurou might be a bit too much.
I see you didn't include Post-Water 7 - or is that what you meant with Water 7+?
Banaro Island
I can see what you were going for with this one, but I think this one should really just be a cut scene.
Thriller Bark+
You already have Perona, Oars and Moria. I think I'd add Ryuma as another NPC! He's basically an alternative to Brook in terms of moves anyway.
Sabaody Archipelago+
Not sure I agree it needs to be a plus. You have plenty of playable characters and Sentomarou and the Pacifista as NPCs, so nothing more needed.
Amazon Lilly
Maybe add Hancock's sisters as NPC's. I'm not sure about this one though.
Impel Down+
No need for any further NPCs than those you already included, I think.
Marineford+
A lot of characters already included. Sengoku could be playable or NPC, both would work for me.
Return to Sabaody
Nothing new needed here, I think.
Fishman Island+
Not sure if those one really needs to be a two-stage arc. If it is, you would probably need a few more NPCs to fight. Aside from Hody (who I would make a playable character), I could Vander Decken, Hyouzou or Zeo being used for NPCs.
Punk Hazard+
If you include Baby 5 in the stage, I think we are good.
Dressrosa+
Phew, so many characters! I already voiced my thoughts about Kyros and Rebecca in my previous post. From the Grand Fleet Army, aside from playable characters Bartolomeo and Cavendish, I could also see Leo and Sai as supporting NPCs.
On the villain side, you have Diamante (who I would make into a playable character), Pica (who I might also make into a playable character) and Trebol as an NPC. I could honestly see almost any member of Doffy's crew making a good NPC, tbh. Sugar would make kinda sense since she's pretty important for the first half of the plot. Senor Pink would make a good choice for an NPC you have to fight with Franky to unlock a cut scene. Gladius, Lao G and Dellinger could all make good NPCs to fight. Only Machvise and Giolla are fully out for me.
Zou
Not much to add here. I could maybe see Pekoms as an additional NPC, but it's not really needed for this arc or Whole Cake Island.
Whole Cake Island+
You've got this covered pretty well actually. Almost all of the supporting cast and the major antagonists are in basically.
Wano Country+
I could see Holdem and/or Babanuki making good NPCs. Denjiro perhaps, too, if you want to include any more of the Red Scabbards.
Onigashima+
Who's Who is a good choice for either an NPC or even a playable character. I'm not so sure about Sasaki though, who ended up kinda underwhelming. Ulti imo would make a really good addition as an NPC at least. I could also see Black Maria as one. Additionally, since you also have Oars as an NPC, how about including one of the Numbers?
Man it took me a lot longer to write these posts than I anticipated. But it was fun! I hope we get a Pirate Warriors 5 some day.
)
Regarding Rayleigh, yeah, I guess that is a bit contradictory. The difference for me is that Urouge and Bonney will probably still have their moments in the sun yet in the story, which is when we will also see more what they are capable of. Whereas I feel like we have seen all there is to see about Rayleigh's fighting abilities, so might as well add him in now. It's not that he would be the most fun character to play, he's kind of the same category as Garp for me. Badass old geezer that would deserve to be in there when it comes to plot importance and technically has the fighting skills to justify an inclusion. But it's also not a character I necessarily need.