Below is a list of what's been changed/added in Alpha 3. I really didn't keep a list like I probably should have so may miss something's off here :p
1 ) Scenes - There's been a total of 7 new scenes added, was supposed to be 8 but it needed a rework so will add it into Alpha 4
2 ) Intro Rework - I'm considering Alpha 3 to be the start of the FM integration, as such, I redid the intro to match more to FM's style.
3 ) Fast Travel - Not total without it's flaws, but it seems to work fine, if you do come across any errors with it, let me know =]
4 ) Spelling/Grammar - Had quite a few issues with spelling, but should all be sorted now.