Seems to be a lot of visual gags in the series from the start. You can tell they didn't expect the show to blow up like it did and it caught them off guard.
To be fair, you have to have a very high IQ to understand Rick and Morty. The humour is extremely subtle, and without a solid grasp of theoretical physics most of the jokes will go over a typical viewer's head. There's also Rick's nihilistic outlook, which is deftly woven into his characterisation- his personal philosophy draws heavily from Narodnaya Volya literature, for instance.