Yeah they definitely were. If you compare both versions back to back you'll see quite impressive things about the sms/ game gear versions. All stages are totally different, some stages "look" totally different and some music are different too. Every floor with the 3 doors, you could actually freely move and pick which order you wanted to complete the stages, while on the genesis it was linear and couldn't move mickey in the level select hub but moved himself from one to the next. I don't think you could pick things up and throw in the genesis version like u could in the sms version. But then again u couldn't throw balls in the sms version. In most of the cases it was simply better on sms for me.
It indeed doesn't get much attention. Just like in that diary video, most of the things are inspired from the genesis game. You can see him throw the balls. I'm fine with it though. While castle of illusion is a classic, surpassing it shouldn't be too hard. From a technical point it looks basic, especially compared to games like sonic, which for some strange reason they have a hard time emulating the physics/gameplay.