His involvement with the Dinobots and his supposed return in the third season certainly leaves this open as a possibility. He is a sadistic Decepticon mad scientist after all.
He most likely will have something to do with the whole arc, but I suspect that the actual beast mode TFs we will be seeing as part of Beast Hunters will have more to do with THUNDERTRON the lion robot and the Beast Planet he apparently hails from than Shock's experiments.
My consistent hope (and personal canon) for Shockwave is that he is inspired by Cybertronian Mythologies. He's heard of beasts, combiners, space bridges, and other fantastical stories, and seeks more truth in them. Maybe those stories of the Thirteen are actually events that took place, back before the Quintessons stunted the natural growth and evolution of Cybertronians. He seeks to bring their true, destined potential out from within, as surely the information is still alive, yet dormant, in their genetic codes. The Insecticons are creatures that have managed to survive the Quintesson raids, living underground, but they are not just fauna like other creatures (turbofoxes, petro-rabbits, dwellers). They actually are sentient, intelligent, and can change their shape; other Cybertroinian fauna like Ravage, Laserbeak and such, have animalistic proto-forms, but the Insecticons' animal-forms are their alt-forms! Are "beast" Cybertronians limited only to those born under the "Beast" member of the Thirtieen? Or could any Cybertronian, with enough manipulation, be able to convert into an animalistic form? Turns out the Lightning Strike Coalition Force were amongst the first test subjects to find out. Nexus Prime was told to be the "first and greatest" combiner, perhaps his descendants live on. Perhaps if a spark is created in the Well of All Sparks, and it splits into several components, those separated components, if their potential realized, could merge into the being they were originally meant to become. The Quintesson influence has blocked the ease-of-ability to the Gestalts, but Shockwave sought those with specific algorithims in their genetic code, with not only compatible, but fraternal, similarities; perhaps their true being could be released (Bruticus).
I think this is possible. I mean the Dinobots are rumored to be in season 3 and Shockwave created them. Also season 3 or 4 will be called Beast Machines.
I'd vastly prefer for the Beast Hunters to be from Animatron. And I think that's more likely than something from Shockwave
I also hope it is Autobots vs. Star Seekers (vs. Decepticons?), with the second team being from the "Jungle Planet" (I really hope for a new name, different from that or 'Animatron'). I'd love it if the planet was inhabited by descendents of the Beast member of the Thirteen, in the great pilgrimage (alongside the founding of Junkion and Velocitron).
I'm sure the Beast Prime would be brought up at some point in that case. I hope Scourge would show up, and other enjoyable beasts