Mostly cosmetic/marketing, SBE3 has redesigned loading port/gate and a slimmer forend but considering the discounts that will be applied to the SBE2 in preparation for this model I'd consider it to be the better choice. Benellis are great guns, I love mine but they are ridiculously over priced for what you get. If you've never owned one do yourself a favour and buy one used or on sale, that way when the novelty wears off you'll be glad you didn't get suckered into full price.
Also, SBE2's have been around for a while and are proven, SBE3's might need some time to get the kinks out, don't be the early adopter helping them with those kinks.
Patrick