Chrisopher Markus has not made an official announcement or declaration that the inclusion of the ‘Mechanized Organism Designed Only for Killing’ (MODOK) as the villain of Captain America 3. What we should concentrate here is that it is merely something that Markus wants to include without bordering on the ridiculous.
Thor probably summed up the description of MODOK best in Avengers: Earth’s Mightiest Heroes when he proclaimed that it was like a frost Giant sized head on an infant’s body. So we can conjecture that’s the main issue that could make MODOKs inclusion problematic for Markus.
Marcus addresses the issue speaking to SFX with his screenwriting partner Stephen McFeely: “I don’t know if there’s anybody that we had in the wings that we couldn’t pull off. There are people that I’m always wanting to bring in. I want to put Modok into something, but you can’t just drop a giant floating head in! It’s not like “Oh, we have to go talk to this guy – there’s something I should tell you about him first…” [laughs]. Suddenly the whole movie needs to take on that structure in order to accommodate him. I never win that fight!”
Markus seems to speak with a certain conviction that suggests he is up for the challenge of including MODOK. However, with Frank Grillo becoming a household name now, Captain America: The Winter Soldier perfectly set up Crossbones as being seamlessly included in part three as the main antagonist. He is established in the universe, he is a complete bad ass and not a giant floating head with baby limbs.