It kind of depends on who you booked with and how the vouchers and that have been issued for you. I know several years ago, when we booked a package with VH, they gave us separate vouchers for the hotel and park tickets.
The first year we had park tickets separate from our room keys (can't remember why we did that!), by asking at check-in NOT to put the tickets on the room keys, and then had to wait in line at one the parks in order to get the tickets. Pain in the neck really because we wanted to go to the water park the first day, and rather than being able to go straight in, we had to go to one of the four main parks, get vouchers converted into tickets and THEN go to the water park. After that, we just had them added to the room key!
There really is no reason to have the tickets separate, unless perhaps you have a 14-night ticket and are doing 7 nights and WDW, 7 nights somewhere else, or something. It makes life much easier and you don't have to keep hold of so many different pieces of paper/plastic. They are so easily replaceable as well, since all the information is kept on the system.