Yes, as people pointed out, Javik was 100% a part of the main story in the original leaks and datamines of ME3. He was going to be, like, mandatory to take to Thessia and Kai Leng would kidnap him to take back to the Cerberus base, not that dorky Prothean VI.
Remember also that his conversations on the Normandy are also almost the only ones in the entire game that even really hint at the idea of "the conflict" being about organics vs. synthetics - the only other one is that defeated Reaper on Rannoch where it's easy to read it as it just taunting you about your prospects of reconciling the geth and quarians to help in the war effort rather than the overall Reaper motivations. So if you don't have Javik, or any other DLC, the star child's randomly going on about how the whole plot of the series was actually about robots vs animals seems to come out of fucking nowhere.