See, here's the thing. Yes, he's still a Stu and all his compatriots aren't much different. But they're not as bad as we all think. Let's break up Eragon and the others...
Personality-
He actually seems like a slightly above-average guy. His determination is uncommon, and likely fueled by a very un-Stu-ish trait- his foolishness. He can be a genius sometimes- he learned to read in less than a week- but these stints of increased intelligence are rare and short. Most of the time he's as dumb as a brick. How many stupid things has he done? A lot, I tell you what!
Story-
Here's where it gets bad. He's such a cliche in this respect. A guy on a quest for vengeance and then off to save the world. Falls in love with a princess and everything. And there's the over-the-top scene where he gets healed at the Blood-Oath Celebration. Yowch. He gets redemption points when the romance spends most of its time not going his way, when he screws up, and when he reacts like a normal person would in messed up situations. Sometimes, he does things just for show and admits it. He isn't exactly humble- indeed, he's proud to a fault. He has a very "look-at-me" attitude at times- not in the way he is written, but as a person.
Weapons-
His weapon, contrary to popular belief, is not a Sword of Sueness. Brisingr, while indeed a powerful and beautiful blade, is by no means one-of-a-kind. Every single Rider had a sword like his, made of the special metal and given its special enchantments. There are literally hundreds of swords with the same enhancements. Each one is unique in its own fashion, mind you- personally forged by Ruhon to fit a particular Rider's fighting style- but that is to be expected with such important warriors. The biggest difference between Eragon's blade and the literally hundreds of others? His lights on fire. And it was a mistake, too. See? He messed up. And then he messed up again by dropping his blade in surprise. It works to his advantage, however, making a good psychological weapon as well as burning through things made of wood.
Za'roc went to Murtagh. While this blade was used for a time by Eragon, and was indeed quite a thing in comparison to those of the average enemy, it wasn't really that much better. It simply didn't need maintenance.
The falchion was definitely not a Stu weapon. It broke, for Celestia's sake!
His bows. One was very average. The other may have been a Stu-ish weapon, being a personal gift from the Elf Queen and all. But, again, he is a highly important warrior at the time.
Abilities-
Here's where the lad really loses Stu points. He is not suddenly, magically good at fighting. In fact, he sucks when he starts out and continually gets his butt kicked. He builds the skill over time, just like we in the real world would have to. His archery is good because he's been doing it for years- and for survival, at that.
His magic? It followed the same route as his swordsmanship- he started off totally incapable and worked his way up. And his magic, while a powerful tool and weapon, has its limits- he's almost killed himself with it more than once.
While he did work himself up to an extraordinary level of skill, he did so over many months and with a Hell of a lot of practice.
Now, let's look at Arya. She and the others are not so in depth, but let's see...
No redemption on her. She's so Sue we may as well call her Fernflower and turn her loose on the Marlfoxes.
Roran-
Well, he's not so bad. He's just really, really strong and a really, really good person. He fights with a hammer- what kind of Stu uses such a simple, crude, yet effective weapon? He's an average guy in terms of looks. His girlfriend- now wife- is decent, but not Sue by any means. Sure, he survived the wall, but out of necessity to the ripped-from-Star Wars- albeit well-ripped- plot. Maybe it's because he spent most of the series being a minor character, but he's not a Stu.
Nasuada-
May be a slight Sue. However, she must be an exceptional person, or she wouldn't be able to lead the Varden- she is as she is by necessity to the plot. Her relationship with Murtagh, however, loses her some serious brownie points, being very reminiscent of Bella and Edward in my eyes. She isn't perfect, though, and she definitely isn't helpless.
Elva-
Is an enigma. I'm not sure whether to call her Sue. On one hand, tragic past and very adult for a 3-year-old. However, she isn't magically accepted by others- indeed, she is, as would be expected, shunned. Her illness was partially necessary to the plot and partially necessary to Eragon's angstiness later on. She also provides something interesting- a lot of ficcers want to know what happened to her in the end.
Angela-
Another I'm not sure of. On one hand, her abilities are extraordinary- excessive, even. However, she is often dishonorable and tricky, both of which are un-Sue-like qualities...
Solembum-
He would be a Cute Animal Friend, but he's too vicious and sapient for that. He, too, is a trickster. He is also a member of a supposedly mythical race. He may be a Stu, but he isn't featured enough for a real determination.
Brom-
Is no Stu. He may be old and strong and wise, but have you ever met an ancient Stu who actually looked old? Brom looked well into his fifties. Sure he could be a little angsty sometimes, but that was about it. He made mistakes. He screwed up. He even spent a lot of the one book he was in lying.
Orik-
The least Stu-ish of the main characters. Orik gets drunk. He's unrefined. He's a mostly-average guy until he gets the throne. He curses, he eats like a pig. He even gets mad when it's not entirely justified! Besides, what sort of Stu would a Dwarf make?
Nar Grahzvog-
Is a big, ugly Urgal. Definitely not a Stu. He is sophisticated in his own way. He is quite bright, actually. He isn't particularly eloquent, however, and can sometimes be a little unaccepting and often misunderstands things from human, Dwarvish, or Elvish culture.
So, maybe Eragon and the Inheritance Cycle aren't as bad as we thought? Opinions, anyone?