It was supposedly mentioned during it's early promotion that Kuuga was based on notes Ishinomori had left behind for an anniversary Rider. Whenever I've seen it brought up it seems to vary as to whether it was meant to be for the 25th anniversary (which was two years before he died, in which case I guess he couldn't get it greenlit) or the 30th (which he sadly didn't live to see). Either way, these supposed notes have never been made public so there's no way of knowing what Ishinomori intended or how much of what we saw on screen was based on his ideas. For all we know, it could just have been made up by the marketing dept.
There's always been a rumour that Hibiki was based around a manga concept that Ishinomori left behind (although he intended for it to be it's own thing, not a Rider). Again, I've never seen anything that proves or disproves this.
If he'd still been alive, Heisei Rider would not exist as we know it. After all, regardless of how much truth there is in the above rumours, all the Heisei Rider shows were made with other people at the wheel. I suspect he wouldn't have liked having Riders with non-insect themes or getting really gimmick-heavy. But then again, who knows? After all, ZO and J were bankrolled and "co-produced" by Bandai. Without the push from the commercial side it's a lot more likely that Heisei Rider might have ended pretty quickly. After all, Showa Rider had it's initial five year stint and thereafter never managed to stay on the air for more than two straight years. Heck, he was still making new TV shows right until the end; Maybe we'd have had a lot less Rider but a variety of other toku shows partnering Sentai on Sunday mornings?