So. Perceptions of the Three Kingdoms is a millennia-old controversy that continues to the present day, and it has much to do with the politics of the time. I'd like to get this out of the way before going in depth with the other questions, to put our biases and the biases of the sources and cultural portrayals in context.

The political controversy that is the Three Kingdoms began when Cao Pi, son of Cao Cao, accepted the abdication of the last Han emperor Liu Xie and proclaimed himself to be emperor of Wei in 220. I say accepted, since Cao Pi refused three times before taking the throne, but it is generally accepted that his faction has engineered the whole ritual and basically forced the Han emperor to abdicate, and Cao Pi made a show to appear humble and unwilling so he wouldn't be seen as an usurper.

When the news of Cao Pi's ascension reached Liu Bei in the land of Shu, he interpreted the events as Cao Pi forcing Liu Xie off the throne and murdering him. This is not true as Cao Pi named Liu Xie as a duke and allowed him all the privileges he enjoyed as an emperor. Whether this is just a game of telephone gone wrong or Liu Bei was intentionally distorting the information he got, we don't know, but Liu Bei took this opportunity to declare himself emperor as the legitimate successor of the Han. (I haven't got into the question of Liu Bei's character but already we have a taste of what he might have been like.)

So the stage is set, both Cao Pi and Liu Bei were calling themselves the only legitimate successor of the Han, while Sun Quan was then allied with Cao Pi. Sun Quan would later declare himself to be the emperor of Wu in 229 so he can place himself equal to the other two rival claimants, but the Wu were never considered as a successor to Han, morally and politically speaking. As we know, Wei ended up conquering Shu in 263 before being overthrown in 265 by the Jin very much like how Cao Pi overthrew Liu Xian. The Jin then conquered Wu in 280 and briefly reunited China. Since Jin was the successor of Wei, contemporary historians considered the line of succession as Han -> Wei -> Jin. This was accepted as orthodox all the way into the Song dynasty, and the compiler Sima Guang used Wei year names and titles to refer to Three Kingdom dates without much controversy.

This changed soon after that, when the Jurchens chased the Song out of northern China in 1127, capturing its capital and emperor. The remnant Southern Song now found themselves in a situation similar to what Shu Han had been going through, a self-proclaimed "legitimate" successor of a former dynasty trying to reclaim its lost territory. The literati started to identify with Shu instead, and even attacked the Zizhi Tongjian for using Wei names and giving Wei legitimacy instead of Shu. Add this to the existing local sympathies to Shu and Wu in the south (where the Song court fled to), and we get a whole culture generating and propagating folklore and performance art from Shu's point of view.

By the time the Mongols of the Yuan dynasty rolled around and knocked the Southern Song off, southern folk traditions had already taken hold in the form of storytelling and folk opera shows. Since Cao Cao and his state were already vilified, the folk just took what they knew from the Three Kingdoms and glorified their Shu heroes at the expense of Wei and Wu. Luo Guanzhong took these folk traditions and combined them with parts of the Records, giving us the novel everyone in China today knows about, the Romance of the Three Kingdoms, published in early Ming Dynasty. Then in the Qing dynasty the Mao Zonggang made further changes to the text to make it conform more closely to the Confucian code, resulting in further glorification of Liu Bei's camp at the expense of Wei and Wu. This is the Romance of the Three Kingdoms we have today.

In Japan, which is where the Koei games like Dynasty Warrior were made, the Three Kingdoms saga underwent one more change: Yoshikawa Eiji published his version of the Three Kingdoms in the 1940s, Sangokushi, before the proper translation of the Romance. Yoshikawa's version further reduced the plot, condensing it to as a conflict between Zhuge Liang and Cao Cao, ending the novel when Zhuge Liang dies. However, Yoshikawa was more balanced in compared to his predecessors as he also wrote positively of Cao Cao. This version was so prevalent in Japan that when the proper translation was published, it actually received complaints because it was so different from the Yoshikawa that the Japanese were used to. Koei's RoTK game series and their spinoffs used to follow Yoshikawa's version, but gradually introduced more historical viewpoints. (This is probably why it took 6 Dynasty Warrior games before Jin became its own faction and we got more historical stages after Wuzhang Plains)

So I hope I have established the inherent biases of the novels, which bled into the games. In China, there is some backlash against these biases, which began as Mao Zedong's brand of Communism put him against the traditional Confucianism viewpoint. Mao loved the Romance of the Three Kingdoms, even proclaiming that he based his war strategy on the book, and professed that he admired Cao Cao the most. This caused a historiographical shift towards Wei as writers denounced Liu Bei, who, by then, was backed by centuries of Confucian orthodoxy. On the other hand, this shift encouraged a more balanced perspective when looking at the Three Kingdoms after Mao Zedong died.

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With all that out of the way, let's get into the sources and actually answer your questions:

1. Was Liu Bei a backstabbing bastard?

Well, he wasn't born out of wedlock. More seriously, he was a product of the times, putting his own interests above those that he was allied to. Of all his former allies, he had not stabbed Cao Cao, Yuan Shao, and Sun Quan in the back, only packing his bags and left as an independent force. Think of the alternative, he could have defected, but he didn't. He left Cao Cao's patronage to be independent, only to face retaliation by Cao Cao, sending him to seek refuge under Yuan Shao. Before the clash at Guandu, he was tasked to disturb Cao Cao's rear, but he was defeated and had to flee to Liu Biao. Liu Biao welcomed him, but was wary enough of him to put him at arm's reach. When Liu Biao died, Cao Cao brought his massive army down to Jing province, and Liu Bei had to seek help from Sun Quan. After the win at Red Cliffs, Liu Bei was able to snatch cities that Cao Cao left behind before Sun Quan could get to them, and from there Liu Bei headed west into Shu, which was Liu Zhang's domain. So far no major betrayal, just opportunism. However, Liu Bei's takeover of Liu Zhang's lands was truly a backstab, since Liu Zhang welcomed him with open arms and Liu Bei ultimately attacked him after an initial show of unwillingness (or crocodile tears, you may say).

2. Zhang Fei

His popular portrayal as a brute is a product of folklore and fiction. His abduction of Lady Xiahou happened in 200, when Liu Bei was causing trouble in Cao Cao's rear during the Guandu standoff. It was recorded that Lady Xiahou was out chopping wood when Zhang Fei chanced upon her and took her as his wife after finding out she's "from a good family" (良家女). Take this however you may, though this shouldn't come as a surprise in times of war.

3. Gan Ning

He was a river pirate seeking for fortune, so yes he did. But he then grew tired of his ways and started studying, so that's cool.

There's also the story of him getting so mad at a servant that the servant fled to Lu Meng's place. Lu Meng asked Gan Ning to spare the servant's life, and Gan Ning said ok. However, Gan Ning then tied the servant to a tree and shot him to death with arrows. Lu Meng was so angry at this he almost went and killed Gan Ning, but his mom talked him out of it and instead he pretended nothing had happened, inviting him to dinner. Gan Ning wept in shame. Take this how you will.

4. Positive qualities

Say what you may about Liu Bei's crew, most of them are fiercely loyal to him. Some stories are celebrated for good reason, for example, despite Guan Yu having such a poor record, no one can dispute his loyalty to Liu Bei - he had no reason to follow Liu Bei when he was so well-treated by Cao Cao, yet he did. Zhuge Liang had no selfish reason to be giving his life to an inept leader like Liu Shan like he did, working himself to death (especially when Liu Bei told him he could take Liu Shan's place!), yet he did. Despite Liu Bei's many failures, many followed him and served him as long as they lived. So say what you may, Liu Bei was surely a charismatic person to inspire such loyalty.

Finally, Shu Han had no formal court recorder and historian, unlike Wei and Wu. So many events in Shu simply weren't recorded. This may explain why you weren't able to find much positive things about Shu.