Here's some thoughts.
Season 1:
As with Angel, Season 1 of Buffy merely introduces the characters. Not much goes on here that is essential to the story since most are just standalone episodes. Perhaps the most important stuff is in the two part series premiere (which can be cut down), some development featuring the Master and the Annointed One (if the kid is even important) and some cuts to their scheming. Of course, a big focus of this is probably going to be the Buffy/Angel thing - her discovery that he's a vampire, etc. Then just skip to the season finale.
Welcome to the Hellmouth & The Harvest
Character introductions, etc. Maybe make this something like a first act.
Witch
Introduction of Amy. Not that important of a character, but she does pop up later. Otherwise, skip it.
Teacher's Pet
Skip it.
Never Kill a Boy on the First Date
The Master and the Annointed One prophecy. Actually, the kid never really panned out, so maybe he's not too important.
The Pack
Skip it.
Angel
One of the more important episodes of the season. Definitely work it in.
I Robot, You Jane
Introduction of Jenny Calendar. She'll play in Season 2, so maybe keep an intro to the character if it's necessary (maybe it'll be better for the Season 2 movie)
The Puppet Show, Nightmares & Out of Mind, Out of Sight
Skip it.
Prophecy Girl
Here's your last act and climax.
Season Two. This one might be trickier since it expanded to 22 episodes this season. Definitely focus on the Buffy/Angel relationship, but also remember to include the Giles & Jenny, Xander & Cordelia and Willow & Oz relationships. Also, the animosity between Xander and Angel is fairly important t the outcome of the season as well as Willow's dabbling in witchcraft.
When She Was Bad & Some Assembly Required
These weren't exactly necessary to the season. The first one just seems to cement the finale of the last season and the second episode is pretty unnecessary. I'm thinking Some Assembly Required may include some Giles & Jenny stuff, but not too certain.
School Hard
Introduction of Spike and Dru
Inca Mummy Girl, Reptile Boy, Halloween, Lie to Me, The Dark Age
Fairly unimportant, though these do probably contain some relationship stuff. Oz's first appearance is Inca Mummy Girl (I think).
What's My Line? Part 1 & 2
Not actually too important storywise, but it does feature the into of Kendra, Dru regaining her strength & Spike losing his.
Ted & Bad Eggs
Not much.
Surprise & Innocence
Pretty pivotal stuff. Again, not necessarily in story, but in the Angel/Angelus switch. Maybe you can lump Surprise with What's My Line to make something of a plot. Also, this sets up Angel's ring.
Phases
Willow & Oz
Bewitched, Bothered And Bewildered
Xander & Cordy
Passion
An important episode in the whole Giles & Jenny relationship as well as Angelus.
Killed by Death, I Only Have Eyes For You & Go Fish
Not much here. "I Only Have Eyes For You" builds on why Buffy doesn't kick Angelus' ass in Innocence though.
Becoming, Part 1 & Part 2
Here's the climax.