The prevailing theme(s) with JSK is that they generally fall into one of three categories: Some form of combat sim, schoolgirls, or thinly-veiled incest. That's the setting, if you will. (Like I said previously, the portrayal of "family" members is just another fetish. Some people get off on milk enemas, or whipping, or bukkake, or furries, all of which I find repugnant. Different strokes for different folks,), so the setting is only just a backdrop. Again, typically, there are four different endings (sometimes only three), and the questions asked/answered and the actions taken lead you to the various outcomes.
Typically, there is a Rape ending (dominant), a reverse rape ending (submissive), a love ending, and a "normal" ending. I think, in a nutshell, the difference in programming (which I've also already said I know nothing about) is that in your games, you set difficulty levels, and whether your rack up enough points during the game determines what final scene you get (based on mood, points, location, difficulty level). In JSK games, there is no skill setting, but you have to figure out the proper series of questions/answers and actions to arrive at the various endings.
To answer your other question, I'm going to refer instead to Christine, rather than CwK. PC starts out timid, but has to overcome his timidity to impress Christine, even though she's the dominant NPC for most of the game. I think you could have a dominant end where PC turns the tables on Christine (rape not necessary, although opens up some potentially interesting story branches). submissive end where Christine gets so frustrated with PC she just takes him (again, rape variant - in your setting, the PC just loses and has to start all over), love end where the PC's "energies" (actions) and Christine's actions/energies "feed" of one another into an expanding spiral of frenetic love/lust/one-upsmanship. The "normal" end would be.... I don't know... maybe similar to the "medium" setting on your games.
These are just my interpretations and suggestions. One thing I
DO want to add though... because JSK is a Japanese designer, all the games start out in Moonspeak (kanji), and of course, have all been attacked by the JPM. it takes the diligent efforts of fans to translate to other languages and un-censor them. Not all of them have been. That's yet another thing I like about your (and Shark's and Chaotic's) work.
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NOTE: As you can tell, I tend to be long-winded. Sorry in advance.
I don't really understand Shark's rules for posting links, but I'm going to take a chance and post one here:
http://www.ulmf.org/bbs/showthread.php?t=7889. Currently, that thread there is over 100 pages long. You really only need to go about 6-10 pages in to get a feel for what it's about. The games are all available for download there on the first posting of the first page.
You'd have to ask the community at large, of course, but it seems to me, in my understanding of JSK games, that the "Daydream" sequence would be incorporated as one of the possible endings. It's great as a stand-alone, and I'm sure folks here like the short time span between games, rather than waiting for a year for one, long, multi-part game, but I think you get my gist.
Don't sweat the petty things. And while you're at it... don't pet the sweaty things.