I will do a blog post on FoB3 soon, but key differences:
1) Rules/"Lists" to cover the English Civil War
2) Inclusion of the "Season of Battle" simple campaign system
3) UI per unit changes slightly to 4 for Infantry and Cavalry, 3 for Artillery. Units are now removed at zero UI.
4) Sequence deck compositions change, and now there are only three, Poor, Average, and Skilled. The only difference between them are the number of Lull and Leadership Cards: Poor 3 Lull, 3 Leadership, Average 2 Lull, 4 Leadership, and Skilled 1 Lull and 5 Leadership.
5) The definition of the Leadership Card changes, and now includes Maneuvering (the Maneuver card is gone!), and "Daring Deeds".
6) There are clarifications to movement, especially as regards to bridges, Fords, linear obstacles etc, and limits to interpenetration.
7) new Pursuit rules.
Still no Emergency Square rule, but not hard to add (for Napoleonic era) – For example, roll the Defense die type of the infantry against the Defense Die Type of the attacking cavalry, if the infantry win, they form square; if not they don't (no penalty for the attempt). If you want to get fancy, you can add a modifier – Cavalry charged from less than 6", Infantry Down 1, 6.1-12 " no change, 12.1 – 24" Infantry Up 1, 24.1 – 36" Infantry Up 2. Easy-peasy!