I am comparing the same options. Park hopper tickets/room/meal plan. 5 day park hopper tickets are $500/person (including tax) if purchased separately, so I would expect the hotel vacation package to show about that same price. I don't see paying a lot of extra money for those "Magical Extras" that would appear to be of only nominal value.
If you look in your cart when you choose tickets/room/meal plan you can easily see the difference in price between NO park tickets and the 5 day park hopper which is a LOT more then $500/person. Assumed others would have noticed this so that is why I am asking the question.
It sounds like, perhaps, you are not accounting for the cost of the dining plan. If you put a room/ticket/dining package in your cart and then remove the tickets, the dining plan is automatically removed as well which would explain why you are seeing such a precipitous drop in the price.
I just priced out 5 nights, 2 adults, AoA Little Mermaid room for 9/16 - 9/21 and got:
Room-only: $995.65
Room with 5-day PH: $1,999.54 (difference of $1,003.89 to account for tickets added)
Room with 5-day PH and
DDP: $2,754.42 (difference of $1758.77 which equals $1003.89 for the tickets and $754.88 which is the cost for 2 adults on DDP for 5 nights)
Edited this package and pull the tickets off and the dining plan comes off, too.
Here is an idea. If you would like to purchase a package which comes with the magical extras, but save some money on your tickets, call in your reservation and ask for a "ticketless package". This is the only way you can book a room+dining package (it can't be done online). Then buy your tickets from a reputable reseller like Undercover Tourist (I use them a lot). Currently, their 5-day PH is $40 less than purchasing it from Disney. Depending on how many you have in your group, that $40 can add up really fast!