These two things (Toads and bosses) and more have been suggested multiple times. Unfortunately, as much as it would be awesome to have them, Runouw has clearly said that his main focus is on Last Legacy right now. This means that is most unlikely to see any new update to Super Mario 63 (even though it has happened already to add Thwomps and Flamethrowers).
But now, people have been doing fine without them for a long time. Several replacements have been found: like using disabled penguins (or any enemy, but penguins are by far the most popular choice, because they are cute) as your companions instead of Toads, and have a sign to display the dialogue...
As for bosses, the most popular and famous alternative is the Block Boss, also known as Bloss: people use rotating blocks that move in a very specific pattern to create an original boss sprite. Obviously, this alternative seems quite limited, but people keep finding new ways to make great bosses. The best examples of Bloss battles I can think of are:
*according to this topicMP3 EDIT: I approve :3
BY EDIT: Me too. : P
There are a lot more than that. If you want to see more, check that topic I linked to above for a list of all the best Blosses (note that the reason I mentioned only these 3 levels is because most Blosses are part of a larger level, whereas these three levels are only focused on the battle, so better examples).