It was mentioned that DIO couldn't use his old vampire techniques (such as blood freezing) in part 3, since his body from the neck down isn't his. However, this game has DIO and Shadow DIO still able to use Space Ripper Stingy Eyes, which makes sense as the head and half of the neck is obviously still DIO's.
If you let the timer run out on the continue screen, Daniel D'Arby will turn your character into a poker chip. In the main series, his stand would do this to his target once they felt completely defeated. By allowing yourself to get a Game Over, you are telling him that you are defeated.
Kakyoin's ending has him passing away from his injuries shortly after the plane to Japan takes off, with Jotaro calling out his name in a panic. The estimated flight time from Cairo to Tokyo is approximately 14 hours, which means Jotaro had to sit next to a dead friend for 14 hours and cannot do anything about it.
A passenger dying would likely cause an emergency landing, but theres still the fact that Jotaro has a friend die right next to him and theres nothing he can do.
If you set up a match between Joseph and Dio, Dio drains the blood of a woman's corpse (if it was Jotaro vs. Dio, it's Joseph who gets his blood drained). It's hard to see, but it looks like Lisa Lisa. It could just be a stranger, but neither option makes sense because Dio needs the blood of a Joestar to revitalize him and Lisa Lisa is not a biological Joestar. Jotaro would have easily been a good substitute in that case.
It could be a reference to how Straits tried to hold a woman hostage to stop Joseph at the start of Part II.
Dio requires Joestar Blood to augment himself and synchronize with Jonathan's body. Draining blood from others simply allows him to heal and get ready for a fight. Heck, he used a woman's blood to repair his leg and stomach when going up against Jotaro.