Shantae/WMG

Risky Boots is actually Shantae's mother.
Could explain why there's an obvious connection between the two.
 * Genies are Always Female in this 'verse, though, and Risky's not a genie. Since Shantae is half-genie, it would have to be her father who was mortal.

The third Shantae game will have multiple playable characters.

 * Given that, and given all her talk in the game about teamwork and relying on one's friends, it's possible (likely? I don't know) that the next game will feature the supporting cast in a much more active role. Considering some of the useful abilities they have (Bolo's weaponry, Sky's trained hawk, Mimic's scientific and mechanical knowhow, and... whatever Rotty brings to the table), it would make sense --   -- for Shantae to be able to do more than ask them for advice. Now the question is whether WayForward would rather go the Lost Vikings route or the Castlevania III route on this... Personally, I think they could handle a Teamwork Puzzle Game quite easily.
 * Jossed, but does happen in the 4th game.

Rotty Tops and her brothers
Given that they were all, and Rotty Tops in particular, it seems likely. In particular, as above, Rotty would likely be a main character, and her brothers would likely be support.
 * Confirmed, more or less.

Risky Boots and the Tinkerbats set up a blockade on the nearest source of coffee.
It would certainly explain why there's exactly one source of coffee beans in the entirety of Risky's Revenge, and it's a long-abandoned storage area. The purpose is, naturally,

The third game will revolve at least partially around Shantae's quest to find out more about her past.
Fairly straightforward, given the ending of Risky's Revenge.
 * Confirmed

The reason Rotty wants to eat Shantae's brain is because she is in love with Shantae
Given popular culture's usual depiction of zombies, one would assume that were Rotty to actually get her wish and consume Shantae's brain, this would cause Shantae to become a zombie - which would mean the two could be together. An odd theory, but then, a lot of the franchise's lore is odd.