Arrg...the only thing I didn't like was how short the chapters are! I'm glad you didn't take too long to deal with his younger years...I'm always eager in AU stories for him to get to Hogwarts.
Speaking of, how are you going to handle what happened in the first five years? One thing I hope you take advantage of is seriousness. I hope you pull off the war as being gruesomely realistic.
Philosopher's Stone: Was the Stone only a test for Harry? Will Dumbledore have killed Quirrell himself? Will Voldemort have made off with the stone?
My hunch/suggestion: Ron and Hermione won't be friends, so no one will discover Fluffy. Dumbledore or Snape will end the threat. If it's Dumbledore, I don't know if he'll do it at the beginning of the year or when Quirrell makes for the Stone at the end.
Chamber of Secrets: I assume Malfoy will still slip Ginny the diary, but who the hell is supposed to save her?
My hunch/suggestion: In canon, Dumbledore probably used Legilimency on Harry to discover that he was a parseltongue, making him think of using the petrifications as another test. However, with Harry gone, I think Dumbledore will take a much more active role in stopping the threat. There is NO believable way that I can think of for them to stop Riddle once he's got Ginny in the Chamber. Dumbledore will have to discover the diary early.
Prisoner of Azkaban: Will Sirius come to Dumbledore for help? He's after Pettigrew, so he'd still escape as soon as he saw the article. Has he been given the Dementor's Kiss? Will Snape let the secret out that Lupin's a werewolf?
My hunch/suggestion: Sirius finds and kills Peter, then presents the body to Dumbledore. Either Fudge believes it or he doesn't. An alternate version would feature Sirius being caught and administered Veritaserum, or possibly just being caught and given the Kiss. Now that I think about it, you'll probably have to have Sirius either die or stay on the run somehow, because if his name was cleared he'd try to get Harry back for sure. I think Snape won't have a reason to let Lupin's secret slip, so he'll stay.
Goblet of Fire: Unless Voldemort came back at the end of first year, I assume he'll manage it in this situation. Whose wand did Barty Crouch Jr. steal? Did they bother entering another student in or did they just back Cedric? If so, who'd they enter?
My hunch/suggestion: Voldemort will kill a teacher and use Crouch to imitate the replacement. If he used him to imitate a returning teacher, then it's far too likely that he'd be caught. Crouch won't submit an extra student, and he won't favor Cedric more than telling him about the dragons. He'll also help him through the maze like he helped Harry. The Cup is a portkey, Voldemort rises, Voldemort kills Cedric.
Order of the Phoenix: Will Dumbledore even know that Voldemort's back without Harry to return? Will Voldemort literally have EVERY advantage in the war? What about Umbridge? Will Fudge still attempt to force her on the school? Will there be a DA?
My hunch/suggestion: No effing idea. Too much depends on how you handle the previous books. However, if Dumbledore knows about Voldemort's return, then he's much more likely to attempt to retrieve Harry early, which you've already said doesn't happen. I think you might have to have Voldemort working in secret to get the Prophecy, which won't take him long, and then trying to hunt Harry down. Whether he succeeds in either endeavor is, of course, up to you. Actually, everything is up to you. This is just my...well...it's sure as hell more than two cents, but you get the idea.
As for relationships...hmm...it's a tough one. If he avoids superficiality, I might say someone like Luna. But then again, I'm always happy to see several other varieties. If he's 16, then he's in his sixth year. I'll keep my recommendations according to who's eligible. Here's a list of people I wouldn't mind seeing:
Luna: Don't do it unless you think you can write her effectively. She's a tough character to mess around with, but if you can do her justice, then I'd love to read it.
Susan/Hannah: Either one them or a Hufflepuff OC would be interesting. It gives you a ton of freedom with the characters since so little of them is seen in canon.
Tracey/Daphne: Again, either one of them or a Slytherin OC. More possibilities. The only thing it'll affect is Harry's relationship with the other houses.
Katie Bell: I just don't think there are enough Harry/Katie fics in the world.
Padma Patil: Same thing, basically.
A lot of that is going to depend on where Harry's sorted, so we'll just have to see. I hope he plays Quidditch!
Well, I've given you plenty to think about (too much, I'd say), so thanks for writing as well as reading all of this crap. Looking forward to your next update.