Protagonist vs. Antagonist (Specific Type)
 

Yeah we've all seen them, the evil bad guy killing everybody and the good guy hero that saves the world. Well I'm tired of this.

I'm looking for a story in which there is no right and wrong. The protagonist and antagonist are both fighting for what they believe is right. I am not looking for an "anti-hero" protagonist. I'm looking for an anime where the viewer can relate to both sides and agree with both sides.

An example would be Death Note, in which I'll say Light is the protagonist (but also an anti-hero) and L is the antagonist. Light is trying to change the world, L is trying to catch Light. Either one's view of the end is "good", but the viewer could agree with either. Or this could be Code Geass, just replace Light with Lelouch and L with Suzaku in the above paragraph.

tl;dr : I want an anime with a Protagonist vs. Antagonist type scenario, but neither side is justified as right.

Fate/Zero, Phantom: Requiem for the Phantom, and Speed Grapher I'm sure has what you need.

It's really long but Legend of the Galactic Heroes is exactly what you are looking for. It is also a classic

The two protagonists are on opposite sides but I think the audience cares about both of them and can see both of their sides.

[C] The Money of Soul and Possibility Control - both the main characters are fighting for either the present or for the future

Seconding Fate/Zero for sure.

Others:
Shakugan no Shana III (Final), while the other 2 seasons build up to it, and they aren't one at this point, it becomes one in the third season. As the tone of the final season is fairly different because it's Protagonist vs. Antagonist type scenario.

Seirei no Moribito it's Balsa acting on the Queen's wishes vs what the Emperor and his court believe is right, although...

I'll third Fate Zero and add Shiki

Tytania and Rinne no Lagrange

Isn't a bit early to call that since the second half just started?

I can only think of these two,
The Legend of the Glass Fleet
Toward the Terra

Planetes might be another possibility. Though it's a subplot, the conflict between the terrorists and the corporate pro-space forces have good arguments on both their sides.

I'll also suggest Miyazaki's Mononoke Hime. The Lady Eboshi is a very complicated and often admirable antagonist, one who puts caring for humans ahead of caring for the environment. To his credit, Miyazaki doesn't provide any easy answers to the conflict between humans and nature, either.

Fate/Zero
Mahou Shoujo Madoka★Magica for me personally it is hard to call main antagonist evil.
Mirai Nikki almost everyone are fucked up in their head and have their goals. Main charas goal was the least of my interest.
Phantom: Requiem for the Phantom everyone had their own beliefs despite being assassins.
Shiki, especially towards the end you start to wonder just who is a real monster here.

I have to second Legend of Galactic Heroes. It pretty much perfectly epitomizes what you said you're looking for, though I'm going to go out on a limb and say what you say and what you're actually looking for are two very different things based on your referencing Death Note. Legend of Galactic Heroes isn't for everyone. It's a lot, and I do mean, a lot of talking. Throw any conceptions of a lot of talking out the window, as it likely pales in comparison to the reality. We're not talking about mainstream shounen type of talking like Death Note, either.

If I was to step into your shoes, Code Geass would be the most obvious show similar to what you liked about Death Note (which is presumably the touted moral ambiguity), but I have a hard time believing you haven't seen it. So, if I had to go with a less mainstream title in a similar vein...hrm...perhaps Blade of the Immortal? Basically, think samurai, moral ambiguity, antagonists you can sympathize with, lots of violence. Also, a negative, no conclusion, as it's based off a part of a manga, and seems like was planned for multiple seasons that never developed.

While Gundam does try to force a portrayal of good vs evil, it's usually actually very ambiguous as to anyone actually being good in most of the numerous Gundam iterations, and I know I can't possibly be the only one who almost always feels more sympathy and empathy for the 'villains'. :heh:

Gungrave is old enough that it's possible you haven't seen it. For its time, it was probably a pre-eminent morally ambiguous mainstream anime, involving numerous characters who are cut from such cloths as gangsters, murderers, etc. You're supposed to like them all though (well, all but one, perhaps, and even he's got his 'aww' moments).

A newer, but not quite current, mainstream anime that is also full of morally ambiguous characters you can get behind, whether they are the protagonists or antagonists, would be Black Lagoon, though only in a few of its arcs, as some arcs do NOT have sympathetic antagonists.

I second this recommendation particularly with regard to the final arc of the second season, "Fujiyama Gangsta Paradise." The antagonist, if you can call her that, is a very endearing high-school girl. Being voiced by Kuwashima Houko only enhances her appeal.

Gundam Seed comes to mind.

Best friends find themselves on opposite sides of a conflict neither of them wanted. Where both sides commit atrocities and the conflict continually escalates.

I couldn't get enough of Kira and Athrun's interactions during battle.

I'm kinda looking for the same thing so might as well post in here. Fate/Zero seems very interesting but is it necessary to watch Fate/Stay Night before to understand things fully?

it's a prequel. so not really, there is a clear connection, but you don't need to see it, imo.

You don't have to watch Fate/Stay Night to watch Fate Zero. But if you are going to watch it after Fate Zero then I would recommend that you watch FSN before FZ. And if you are planning on not watching FSN at all then there's no need to watch it. FZ is completely independent of FSN.