Some insight into what Ive learned. There are
Alterered Beast
Sonic (Leader... Red markings)
Sonic (Leader... White markings)
Sonic system
Core
Streets of Rage 2
Sonic 2
Toys R Us
Canadian
Canadian 2
8 different box variants for the U.S. version that I am seeing and 2 different Canadian ones. This is only for the Model 1 (1601 model). I believe the Altered Beast one was the only option until Sonic was released, then your only option was the Sonic pack-in for a while until they gave you the option to buy either the "Core" or the Sonic pack in- at which point I believe this is when they stopped putting red markings on the controller. At one point along the line, there was a Fighting System that came with Streets of Rage 2 and there was also a Toys R Us exclusive one. There was also a "Sonic System" and "Sonic 2 System". The one that came with Sonic 2 I am guessing is the last bundle that they made because I am thinking the Model 2 Genesis came out around that time. I havent gotten that far yet...