Will they continue the same prrks that are currently offered such as EMH, 60 day FP+ window?
No one knows. My guess is that eventually those will end, because they just got rid of the EMH access at the Hilton Lake Buena Vista, and that was part of the same deal as far as I know. The Swan, Dolphin and the Hilton WDW were all built by Tishman, the primary construction company for Epcot. Part of the deal they struck was that their properties got special perks, most notably EMH. All three are still owned by Tishman, as far as I know, but while the Swan and Dolphin are still managed by Tishman, I believe the Hilton LBV is managed by Hilton.
Wait, you said Marriott is taking over all Starwood properties?
Sort of. Marriott is buying Starwood. Both of these are hotel brand companies. So all the Starwood brands (Sheraton, Westin, etc.) will become Marriott brands. One assumes at some point Starwood Preferred Guest will merge with Marriott's own program. They are not necessarily taking over the properties, except the ones that are actually owned by Starwood. Most of the hotels will continue to be owned by whoever owns them now.
See, with a hotel, you have to distinguish between the brand, the management company, and the owner. Those can (and often are) three completely different companies. The owner actually owns the property (the physical building and land). The management company is who the people who work at the hotel work for, and that company typically works under contract for the owner. The brand just licenses the brand name and sets brand standards. It's a franchise system.
It gets complicated because the management company can be a division of the owner (as in the case of Swan & Dolphin, where Tishman is the manager and owner) or the management company can be a division of the brand (as with the Doubletree Suites LBV or the Hilton Bonnet Creek, which are managed by Hilton), or it can be a completely separate company. There are even some hotels where the owner, management company, and brand are all the same, but that's actually a fairly rare situation.
I hope this isn't way more than you wanted to know.
