Things would've played out the same way they did, just with minor differences and different timing. Consider what actually happened:
-When Vince returned after the limo explosion, he said he faked his death to see who really cared about him (but this didn't lead anywhere), and then he was informed of an illigimate long lost child. That was going to be Mr Kennedy, but because he was suspended, it ended up being Hornswaggle and the storyline was scrapped.
-The next year, the stage collapsed on Vince. This could be seen as a restart of the death angle.
-When he came back, he entered into a fued with Randy Orton, where Orton was going after the entire McMahon family, eventually leading to Triple H being revealed as Vince's son-in-law and defending the McMahon family.
The original plan would've combined elements of all of these. He would've returned to reveal that he faked his death because he wanted to see who really cared for him, which would've eventually lead to the discovery that he had a lost long child. And since Shane and Stephanie didn't care about him, this 3rd child would get his love, support, control of the WWE, etc. Eventually it would've been revealed as Mr Kennedy (if he was never suspended), who would've had the same fued with the McMahons that Randy Orton did. It would've been revealed that he faked the test results(he wasn't really his son), but there was nothing the McMahons could do because he already had part ownership or whatever(much like there was nothing they could to Orton because he had a guaranteed title shot at WM thanks to his Royal Rumble win). Eventually Triple H would've stepped in to defend them, leading to Kennedy vs. Triple H at Wrestlemania.
You don't just completely scrap massive storylines like that. A lot of time and effort was put into the planning, and obviously they really liked what they had. So everything eventually played out like it would have, all the major plot points still took place, just with slight adjustments along the way.