Step 1: Get rid of Battle Regimens. They're incredibly clunky.

Step 2: Bring back manual skillchains. Feel free to vary the effects and such, and apply some of the BR effects if you want. Allow mages to participate, and even create their own chains. Yes, this means letting mages skillchain positive spells onto party members for cool effects in addition to simply chaining on mobs. Protect + Shell = Reflect might be cool, for example.

Step 3: If adding auto-attack, make sure that toggled "next attack" buffs apply to manually-triggered skills only. This way there is no worry about wasting a buff on an auto-swing while waiting for stamina or TP to recharge.

Step 4: Make auto-attack easily toggleable and the on/off function responsive, unlike in FFXI where it was toggleable, but took forever to go from attacking -> not attacking -> attacking again.

Note that steps 1 and 2 are independent of auto-attack, and my opinion of something needs to happen regardless.