just think of them as expansion packs
besides, it got top quality contents no doubt
fair deal imo
They actually are expansion packs. I've talked with plenty of people but this is how majikoi is and this is the general conscientious
the Original: Maji de watashi Ni koi Shinasai which is how it is all supposed to be, and seeing as how the manga and anime all focus on Momoyo, it seems she's the true route and heroine of all of majikoi (plus the story with the flag also suggests it)
the fan disk/ sequals: Maji de watashi ni koi shinasai S, basically, they added more stuff to the old stuff in order to create new stuff. S is only a sequel in the respect that it continues the 5 routes from the original. it's a fan disk when it goes off to the other 5 heroines. basically, that part is for entertainment value, in other words it's not part of the true story, they basically added it in but it does not really part of majikoi and not to be taken seriously. think of it as an expansion pack of sorts with new material just to get more makings out of it.
the expansion of the fan disks : Maji de watashi ni koi shinasai A. basically, an expansion of the fan disk to cover the other heroines with ero material. the stories/routes themselves are not to be taken seriously, seeing as how some of them seem highly unlikely from the original majikois view point, and even in some of majikoi S's as well. A is basically just that, to cover the other heroines for entertainment value/
with S and A, it's about entertainment with the whole "What if" value in it's new content, but the original VN (or even majikoi R) seems to be how maji de watshi ni koi shinasai SHOULD be. the new stuff is marketing/entertainment stuff.
but everyone has their opinions and favourite route/ heroine, so basically its
Maji de watashi ni koi shinsai - Original
Maji de watashi ni koi shinsai S - Sequel/Fan disks/ expansion
Maji de watashi ni koi shinsai A- Expansion
call it what you will.