Here's my 2 cents worth. I'll preface it by saying I am a Disney specialist
travel agent and this is what I recommend for my clients.
Right now, with the MYW plan a package and tickets and room booked separately should be the same price. With the old packages you had to get UPH tickets and for people who didn't go to water parks or Disney quest or who arrived at 8 PM and checked out at 10 am they were paying for lots of stuff they wouldn't use. That isn't the case now with MYW. The package price will be the same as room only and tickets bought through Disney *unless you have a room only code of course. You could save some by buying your tickets from a broker but if you are talking buying through Disney, there shouldn't be a difference now (if you do a quote online and it's $90 more for a package, that is the cost for the optional insurance).
ALWAYS start with room only, even if you are pretty sure you want a package. (I will of course honor a clients wishes if they don't want to go this route).
The reason is that it gives me MUCH more flexibility in finding my client discounts. The cancellation and change policies are SO much better with room only. If you start with a package you must pay your final balance off at 45 days before arrival. Say you book the Poly for 7 nights and you are getting 7 day MYW tickets with park hopping. Now lets say they release AP codes at 44 days before you arrive with $100 off per night at deluxe resorts. With the AP codes you would save $597.32 by buying 1 AP and using the room only code. Since you booked a package, we have to cancel your reservation and rebook room only. Since you are less than 45 days out you are hit with a $100 cancellation fee. You are still $497.32 ahead but can you think of better ways to spend that $100? Now a different scenario...they decide at 30 days before your arrival to release general public codes. They offer them on pacakge deals so you want to apply the code. There is a $50 fee for any change to your package reservation that changes the price after 45 days out. So you essentially lose $50. With a room only booking in either scenario we apply the code and you have no penalty fees. We can convert you from a room only booking to a package booking with one quick easy phone call and we can do it right up untill 5 days before you leave. So if you budget for the package we know it won't be MORE than that price (unless ticket prices go up which we don't expect any time soon since this pricing structure is new). If no better deals come out a week or two before you travel, we call and convert you to a package with no change fees. You have to pay the full balance at that time but you held on to that money all that extra time rather than letting Disney hold on to it.
If you don't have a room only discount code then good use of the dining plan does get you some discount but don't lock yourself in to a package before you have to.
I hope that made sense! I'll go ahead and say that I *do not* recommend this because of something like me making better commission on a room only booking. The commission is better on a package. I recommend it b/c I honestly feel it is better for the client. It's more flexible and allows us to keep our discount options open for as long as possible.
If you weren't getting the dining package, would you still get the MYW package without dining? 
I really, really appreciate it. 
