Aside from legendary version-mascot Pokemon..:
SUN (10 Pokemon families, with all the Pokemon I mentioned as ideas):
I'm hoping that Solrock (holding Sun Stones) and Sun Stone-associated Pokemon are exclusive to Pokemon Sun:
Bellossom, Sunkern/Sunflora, Cottonee/Whimsicott, Petilil/Lilligant, and Helioptile/Heliolisk.
Larvesta/Volcarona would fit really well, although it sucks that there is no proper moon counterpart (I don't think that Cresselia serves as a good counterpart for them)..
Additionally, if you interpret the Shiny Stone as being associated with light (by virtue of its Japanese name, Light Stone), then these Pokemon could also fit: Togetic/Togekiss, Budew/Roselia/Roserade, Minccino/Cinccino, Floette/Florges (could AZ's Floette make an appearance..?).
MOON (10 Pokemon families, with all the Pokemon I mentioned as ideas):
I'm hoping that Lunatone (holding Moon Stones), Cresselia (ugh; but there's no proper solar counterpart!), and Moon Stone-associated Pokemon are exclusive to Pokemon Moon:
Nidoran/Nidoqueen/Nidoking, Clefairy/Clefable; Igglybuff/Jigglypuff/Wigglytuff, Skitty/Delcatty, Munna/Musharna.
Vileplume could probably fit here as well (it honestly seems like a Moon Stone-esque candidate), since it learns Moonlight and Moonblast in contrast to Bellossom's Morning Sun..
Additionally, if you interpret the Dusk Stone as being associated with darkness (by virtue of its Japanese name, Dark Stone), then these Pokemon could also fit: Murkrow/Honchkrow, Misdreavus/Mismagius, Lampent/Chandelure, Honedge/Doublade/Aegislash.
"MIX/ECLIPSE":
(Dang Dawn Stone messing things up even though it's supposed to be "Awakening Stone" by virtue of its Japanese name...I don't know what to do about these Pokemon; probably just throw them in both games as available Pokemon to enforce "unity" of some sort!) - Ralts/Kirlia/Gallade (and Gardevoir); Snorunt/Froslass (and Glalie)
:t196: :t197:
I don't know how you would make Espeon/Umbreon exclusive unless you limit the "time/planetary rotation" in each game to day or night, or you change their evolution method from being clock-based. What I've hoping for is that the "evil team"'s goal is to effect permanent day or night, and proper planetary rotation is only restored either once the player defeats the evil team or beats the Pokemon League/Pokemon Champion completely.. On a side-note, Game Freak should also retcon the evolutionary method for Espeon/Umbreon...they can keep the day/night dependence, but just retcon it so that the Sun Stone and the Moon Stone can induce the same evolutionary changes on Eevee (I mean, it makes so much sense; even Pokemon XD: Gale of Darkness bothers to use the "Sun Shard" and "Moon Shard", which essentially function/act as the same thing/stand-ins for the Sun Stone and the Moon Stone!).
*Wow, even though I feel that Cresselia and Larvesta/Volcarona don't properly counterpart each other, by including them, I managed to come up with 10 Pokemon families being "exclusive" to each version! Neato! {XD}^^ Eh, but Gloom might cause issues unless Pokemon Sun lacks Leaf Stones (and Moon Stones), and Pokemon Moon has Leaf Stones and lacks Sun Stones..
*By version exclusivity for all of the aforementioned Pokemon, I mean (more of the "more common than the other, like Plusle and Minun in Pokemon Ruby/Sapphire" kind, not the "one is obtainable, one is completely unobtainable unless you trade" kind of version exclusivity). {:3} Trading should strictly be a convenience, not mandatory, in my opinion (to account for single-cartridge players without local friends/cartridges and/or Internet connectivity..).