The Friendship didn't get a great edit. April and Ivette blubbered all the time. Jenn came back into the game and pulled a shifty move. The Cappy stuff was portrayed as it really was: freakin' ridiculous. Only Maggie got off well. She was sort of a quiet mastermind on the broadcast show and more of a Godfather type on the feeds.
That's how I saw it, too. In fact, I started reading the feeds thread that year because I couldn't stand the Friendship and the Cappy Cult from watching the aired show.
As I recall it, Nakomis's six-figured plan was pretty well covered on the aired show, as was Dan's game in his first (and winning) season. For last year's season, in some ways we got more of Dan's game in the aired episodes, because they showed Diary Room interviews where he let us know what he was really trying to do. From the feeds, he was shown saying this to Danielle and something totally different to someone else, and there was a lot of discussion about his true loyalties.
For the biggest discrepancy between the feeds and the aired episodes, I've got to go with Season Eight. This season has been bad in that they've covered up a lot of the worst things said, but that's nothing unusual for this show. CBS has not been portraying this final three in anything close to the same heroic way they did Evel Dick. I'm not a big believer in conspiracies of any kind, or that the game is rigged (heavily edited, and lots of DR coaxing, but not rigged), but in that season, I think BB was pushing hard for ED to win.