Agreed. Daniel still has another year of school (along with friend Marco Barrella) and apparently Annie does too. Also, only Mike and Kelly know Annie's true identity and both have now graduated as well as having been sworn to secrecy in the aftermath of all that happened at the grad banquet.
The difference moving forward is that Jane will be out of the picture so some parental figure in Annie's life will have to fill the void, particularly now that she is chronologically younger than even Daniel now. This would likely be Sara but in order for that to happen certain parts of hers and Daniel's memories will have to be wiped clean.
What Annie wants will be key to what happens in the end as Dr. Sky feels like she owes her. Annie knows she is biologically younger than Daniel now and so her future is in a relationship with Daniel who she knows is in love with her rather than with her wife Sara who has adjusted to life without a husband. Since Annie does not want Daniel to feel heartbroken he may be open to being Daniel's girlfriend. For this to happen though, both Daniel and Sara's memory has to be wiped clean of the knowledge that Annie is John Rogers and that she had sex with her own son.
The ending has to deal with these problems while also respecting the fact that the mind specialist Anton Yacko cannot make anyone do something without their consent. Fortunately, Sara and Daniel "want" to forget that Annie is John Rogers and had sex with her son and so that is something Mr. Yacko can wipe from their memories (maybe they are both made to believe that John Rogers died and that Annie is now alone, having been abandoned by family for a second time in her life). If Annie trusts Dr. Sky enough she may also be willing to undergo hypnotherapy to be made to forget she was once married to Sara and is Daniel's father. That would pave the way for Sara, Daniel and Annie to have a relationship but of what kind remains to be seen.
At worst, this would leave open the possibility that Annie becomes a live-in maid to Sarah and Daniel and at best, according to some, an addition to the Rogers household and possible confidante, love-interest of Daniel. Lets not forget that Annie has a penis and Daniel does not know this. Lets not also forget that Jimmy accepts Annie for who she is and Annie has feelings for him.
Based on all of the above, there are some complicated twists and turns for AndreaTG to navigate with this ending but based on all that I have read I have every confidence she will deliver something believable.
If I were to hazard a guess, Anton Yacko fixes everyone's mind in such a way that allows Annie to live with Sara and Daniel, quite possibly as a live-in maid. This will complete the irony in the title of the story - Man of House. On the softer side, Daniel and Annie will develop a relationship as friends not lovers, Daniel eventually leaving for College on a soccer scholarship. This will placate many who never saw this as a story of incest, especially among two unwilling participants. For her part, Annie develops a relationship with Jimmy and may even be hired as a manager for the company. This is tricky given Joe Scally will be the new CEO but he may be open to Annie in this role as he knows she is good at her job. Sara will take comfort in the fond memories she built with a husband she considers deceased, taking joy in Daniel's success as a budding soccer player. Lastly, there will likely be a follow up with Luca turned into a big boob bimbo, maybe even being used by Joe Scally to keep customers "satisfied".
Time will tell.