All units and ctructures have had very signifigant reductions in build time and cost/
All "Top-Secret Protocols" and superweapon abilities recharge in literally 5 seconds.
Several upgrades (e.g. Fortified Fleet, etc.) have had their effects massively improved.
All unit abilites recharge from 5 seconds to instantly, plus some have had their effects super-boosted.
Units added for each faction*
*= How many depends on if I ever get Uprising