I like the gameplay on the LE better but I am biased. I own an LE but have played a friends pro and did not like it nearly as much.
6 ball multiball is only achieved as an add-a-ball function so unless you are good, you rarely see it.
The lifting bridge is a cool effect but actually hurts you in that you cannot progress towards BW during multiball (unless you get VERY lucky and jump the gap with a perfect, fast shot).
The crossover arrow bridge is great in game play as it allows you to repeatedly hit Black Widow and Hawk Eye over and over once you get good at the BW shot.
The Thor drop targets are cool but you really can't see them under the plastic and behind the arrow so you end up looking at the lighted inserts anyway.
The bling - powder coated metallic armor and color changing GI is VERY cool and IMO worth the price of admission. It is a very cool effect when you start Thor mode, the whole machine turns blue, Black Widow, the whole machine turns red, Hulk Green, etc.
I will add the Hawkeye arrow as bling too because it looks so cool!