Of course these are a dime a dozen, but my question is :

in which games with two or more warring factions does the conflict feel authentic to you?

More than that, it really feels like there is a serious conflict going on, and you find yourself caring about the battles the game puts you in because of how it may affect the outcome?

I can only think of two, possibly three examples :

Quake IV - I love this game and in each playthrough I find myself feeling like I'm part of an actual invasion force hoping against hope that the the war can be won without the death of one or two favorite story characters (just like in a favorite film in which you know a favorite actor is about to be killed but you still wish that somehow it won't happen)

Wing Commander IV - It helps that it's basically a movie with gameplay dispersed within. I remember trying all manner of conversation choices and gameplay variations to somehow keep Vagabond from getting killed during one level.

and possibly

Half-life : Opposing Force - Running around the levels with the other soldiers following you somehow felt extremely authentic.

Wasteland 2 between the Atchisons and the Topekans.

I was going to say Warcraft III. I could never really get into the story of Starcraft for whatever reason.

C&C, mostly because of the tacky videos.

Joe Kucan's performance being the glue that held it all together.

from 40k?

Among other things.
Aliens and Starship Troopers were the first two things that came to mind but you can find pieces of it in countless movies, books, games.

I'm a huge RTS fan, and Warcraft 3 is my favorite RTS, yet it doesn't quite manage to convince me of a major conflict being played out before my eyes. Well, perhaps a bit, especially the first and last northrend levels with Arthas. I'm just not sure though. I think the problem is that, as an RTS, it's comes across as too formulaic. But that just comes with the territory for a classic RTS and I don't hold that against it at all. Then again, why did those other missions with Arthas work for me? And I'm not sure I would want to change anything about Warcraft 3 at all. It's undoubtedly one of the top 5 best games I've ever played. So yeah, I'm pretty confused about where I stand with Warcraft 3 when it comes to this question.

I'm not sure I would say that I couldn't get into the story of Starcraft, but I will say that I don't find it nearly as gripping as Warcraft. I did find the world and characters pretty fascinating though. I suppose I should actually make time to actually read Starship Troopers sometime. If only to pay homage to the space soldiers in powered armour idea, which, as a devoted and humble follower of the EMPERAH I'm forever grateful for. If indeed the novel is responsible for it.

But why?

I loved Warcraft and Warcraft 2, but was bitterly disappointed by Warcraft 3. First of all it looked downright hideous for the time. Compare with Armies of Exigo which came out about the same time and looked amazing. Also I was not a fan of the whole RPG element. Heroes, items, etc., all of that took away from the actual RTS formula in my opinion.

The book is bullshit. I'm going to get a lot of crap for that but it really is. Even Heinlein's friends admitted he was an asshole, obsessed with this twisted idea of good versus evil, right and wrong, noble Christian duty to annihilation the godless savages of the uncivilized world, yadda yadda yadda.

Fallout: New Vegas
You see crucified people here and there, encounter NCR and Legion patrols, sometimes fight them and if you choose to join one of the sides (you don't have to, but you can), you will indeed feel the missions you do, the battles you fight on behalf of your faction slowly turning that stalemate. The conflict doesn't feel like something made up just for the sake of being there, it stems from ideological differences of the opponents.

Star Wars: Knights of the Old Republic
Especially if you don't miss that trial sidequest where you have to find out whether a Republican veteran is responsible for the death of a Sith officer - you'll see that those who opposed you from the very start also have some agendas, some ideals and feelings - they aren't just "evil because they are Sith", you're just caught on the opposite sides of this war. And yes, they are too different from your Republic buddies so the conflict feels natural as well.
In that regard The Old Republic (MMO) is probably even better.

XCOM: Enemy Within
Come on, they're wicked space aliens FFS! They kidnap people, kill them, destroy your cities - it's only natural you fight back and if some unlucky non-human motherf-ker gets captured - 'e will go straight to good Dr. Vahlen to be interrogated and never seen alive again. And those EXALT whackos dare collaborate with ALFs? Well, fine, they'll get wiped from the face of the planet as well, the backstabbing nutters!
XCOM 2 takes this even further as it implies that you lost the first war and Earth is effectively conquered by aliens. I'd say this conflict feels authentic enough to me.

Civilization games
Fighting for resources, fighting because your opponent supports your mortal enemy, fighting Gandhi because that pacifist just nuked you... lots of fun to be had here and if you try to play through a game without ever going to war - good luck with that. You'll soon understand why people just can't live peacefully on one planet. :-P

You should absolutely read it. The book is amazing, much like the rest of Heinlein's works.

Fun fact: When I was in the Marines (almost 20 years ago, holy shit the time flies) Starship Troopers was on the Commandant's reading list. I had already read it by then, but it was a pleasant surprise to see actual good literature there.

Oh I think we'll have to agree to disagree on this one in advance. I thought it looked amazing, and along with the phenomenal music and video clips does a great job of creating a believable fantasy world overflowing with atmosphere. And having played Tiberian Sun, Red Alert 2 and AoE2 to death up to that point I welcomed the addition of, to be fair, very light rpg element left over from what the game was originally meant to be : a party based rpg.

It's even more subjective than that however: the whole warcraft vibe simply clicks with me, and with Warcraft 3 the realization of the world reached near perfection for me, which is why I jumped headlong into WoW first chance I got. Though I only lasted 4 or 5 months by which time most of the high level regions no longer felt true to the W3 vibe that I was a fan of. At least up to cataclysm only the vanilla zones really have that same vibe.

I do agree that Armies of Exigo looks amazing, with an incredible trailer to boot.

Alaric loved that book.

This is Jack's complete lack of surprise. :P

I really do like Warcraft as a setting. Naturally I own all the games in the series. And yes, Warcraft 3's cinematics blew me out of the water when I saw them. (Same for Warcraft 2 actually). The music was good, the controls were good, but the graphics ... oh man. Blizzard is always verymuch behind when it comes to the technical aspect, and I do understand that they want their games to run even on calculators, but those 3.5 polygon models were HIDEOUS. I mean, shit, Tottal Annihilition looks ok even today, and it's an older game. Blizzard REALLY dropped the ball when it came to that particular game's visuals.