Okay so you have Willow, and you have your own alternate universe. It's a simple fact that AU fic, especially when on the long side, is looked down upon by the general fic community. Why is this? And how can you avoid the pitfalls of so many other AUs?
My first suggestion is that you keep your fic recognizably Buffyverse. If everything is totally different, often times you end up with an original fic with the BtVS and AtS characters (and usually these aren't really the characters, but original characters wearing their faces) inserted in it, and honestly? Most don't really have a desire to read that.
My favorite sort of alternate universe fics are those that diverge from canon at some point during the actual series. For instance, if Willow had died in "Seeing Red," instead of Tara. These kinds of fics are much like canon-based fics, and are less likely to make readers run screaming. You can usually go about those like you would any ordinary canon-based fic.
There are also fics where one small - or large, like say Willow having never dated Oz - detail has been changed, though everything else stays the same. These kinds of fics - especially when you've changed a fundamental part of a character (Oz's lycanthropy, Angel's vampirism, ect.) can fall very flat very fast. Often what they are defines who they are - they simply would not be the same character otherwise. Now, I'm not trying to say this is taking the easy way out entirely, because every kind of writing has it's own special brand of difficult - but it often *is* taking the easy way out in terms of characterization. I'm not saying you can't ask the question "What if Spike wasn't a vampire?" and attempt to answer it in a fic, and make it good - I'm saying, it will be very, very difficult to keep the character recognizably Spike, and unless you're very secure in your characterization, attempting it is akin to story suicide.
Then there are the fics where everything is different. These can take place in exotic locales ancient or historical or modern or futuristic, with no vampires or demons or slayers. These can be done well, but it is extremely hard. Most writers don't have enough skill to attempt it (though they often do anyway *cough*). I would suggest writing canon-based fic to begin with, and getting secure with the characters, and then branching out to scenarios this AU, if you absolutely have to.
No matter what, make sure your fic makes sense. If Spike is in your fic as an American - ask yourself why is he speaking with a British accent? No one suddenly starts using a British accent for no reason, except perhaps Madonna. If he isn't American, how did he get to America? Why? If Angel has become human in your fic (as opposed to having always been human, which is a different story), why? Why is he human? How? Make sure you can explain everything. Just because it's AU doesn't mean you can skimp on these kinds of things, rather it means you have to be more careful with details like this. It's kind of like how you have to be more careful with the characterization in your AU fic which brings me to . . .
I've read some really horrible alternate universe fics. Why were they horrible? The characters seemed to be original characters wearing Willow and Angel and Buffy and Spike's faces. Now, under different circumstances characters would be slightly different, but it's very important that you don't take the differences too far. One of the major issues are characters that are just so nice and truly wonderful friends, in the AU, to their canon enemies. Even in your alternate universe, you should keep the characters' relationships with each other similar to those on the show. I really doubt Willow and Buffy are going to hate each other in any universe, and to make this so is OOC, borders on character bashing, and results in your fic veering onto 'original character' territory. This does not mean they can't argue, or even become enemies - *any* two characters can become friends or enemies under the right circumstances, AU or not. What I am saying is that at the beginning, don't have them hating on each other, at the beginning show them reacting to each other how they reacted on the show - and then, through events of your choosing, have them grow apart - and grow to hate.
If you're not sure how to write a character - other than Willow (if you want tips on writing Willow, just consult some of the other essays on this site) - as seen on the show, I'd suggest you head on over to the BtVS Writers' Guild for links to sites that can help you with the other characters.
Once your fic is written, make sure you get a good beta reader, maybe even two or more if your fic is on the long side. You won't be sorry.