Flaming arrows are armor piercing, so they'll still work well. Destruction will pop their armor off if you have Earth mages...it's lower level research, but takes multiple mages to get good coverage of the enemy army, as opposed to a one-cast.
Well actually there will probably be fewer armoured chariots ect due to their resource cost but the spells mentioned(flaming arrows and destruction) will work well as will many battle magics(any that cause instant death, have high damage or are armour piercing)
chariots are kinda small as tramplers go... put something big on the flanks, and though you might not do much TO the chariots, they also won't be doing much to you. ("ohnoes! he pushed my vine ogre a lil bit and did a whole 1 point of damage! in only 29 more rounds i'll be in trouble!!!")
large size and lots of hitpoints should keep the chariots busy doing nearly no damage until they build up enough fatigue that you can hurt them.