Each route will be independent and will have its own ending. And yes, that means winning the fight isn't necessary.
However, if you manage to complete all three before the end of the 40 days period, you get a special ending.
I'm not sure I understand -- how can you complete the three routes in 40 days? If you go one route (which I assume means consistently selecting more submissive, 'affectionate', or rebellious answers), how can you also do the other two without loading a previous save which would erase the progress?
By the way, let me join all those who have praised you so far. The art in t his game is excellent, and there is an attention to detail that leaves me very happy. (I noticed that, in your intro, you had music playing as the MC ran to the academy, and we could see various scenes -- it had a cinematic feeling that really made me think of a real movie.) It is quite obvious that you are putting a lot of effort, and a lot of yourself, in this game. I really hope you'll succeed in bringing your vision to life!
I personally have nothing to complain about. The intro is long, but I like it, because it gives you more time with the MC and his circumstances, so you can get more attached to him. (You've made me like him enough that I, aside from wanting to follow the most submissive route to see where it leads, also kinda want him to win in the end -- he seems to be so happy about the chance he got to achieve his goals, you actually want to see him succeed in his studies. I'm even wondering if, despite the title, you'll go so far as actually having an ending in which he escapes as a free man, respected by all the others, and well on his way towards achieving his dreams.)
I see the emphasis on feet, and I am curious about whether or not you'll strive for a balance with other fetishes or not. I'm not complaining -- I do have my own personal preferences; but I am also a firm believer in authorship. I think the best work is obtained when the creator follows the path s/he really prefers -- the dedication level increases, and the result, even if not for everybody, becomes better, deeper, and more meaningful (besides being more fun to produce, and to consume!). So, I'm not complaining; I'm just honestly curious. You've decided on a structure that involves direct contact with 12 ladies, and possibly a number of side quests/stories; are you going to explore various fetishes with each lady and/or side story, or will you concentrate on personality and character development for everybody within a few specific fetishes?
I'll definitely be following the evolution of this game. I wish it -- and you in this, and all future, endeavor(s) -- the best of luck!
(P.S.: Three little mistakes I noticed in the text.
First: After Leah tells MC that they're going outside the campus, he stops her to demand a duel. He then says the following sentence, where the words "anyone that time" are repeated incorrectly: "You know better than anyone else that time anyone that time is a luxury I don't have."
Second: In the first day of art class, the teacher, Amy, says: "irstly, as you can see here,..."; of course, this should be "Firstly,...".
Third: In MC's punishment scene, the narration says: "Leah brtually slams..."; of course, "brtually" should be "brutally".)