The ending of season 2 didn't feel strange to me. At some point in a relationship, one needs to select who they want to be with and be accepted or not. This is a realistic thing; I also think it created a good ending for season 2. You chose and got the girl (or didn't). You also had to break up with whoever you didn't choose, which is a hard thing, but something that healthy individuals do. I felt this capped off the season well.
The point that there are divergent storylines is valid, although I don't know how much it'll impact future games. I've played episode 9 (the first section of season 3), and each character has their own story sections although there are also a lot of overlaps. People can be friends and still have similar interactions with slight variations. I don't see this as too much different from the previous seasons/chapters. It's hard to judge in episode 9 because it was a free roam. Those tend to suck up time attempting to navigate the !@$%@@#$^ rooms. Still, if it's 4-8 hours for that part of the game (it took a while but I don't remember how long), then a single play-through could still be 12-32 hours for the season (assuming 4 chapters). That's for a single play-through as different choices will have different outcomes and allow for many playthroughs.
To some extent, the author is doing more work to produce in the same time frame. They're doing this because they're becoming much more skilled/efficient at what they're doing, and they're upgrading machines and purchasing new machines to render the artwork faster.
What's funny is that the author is adding in new "main girls" for the MC to pursue. So, if people think the argument for consolidating relationships is to simplify the game, I'd hold up the addition of other romantic interests as counterpoints to that argument. Not only are there additional interests, but it appears that "swinging" could happen as well with a number of characters expressing interest in season 3, depending on playthroughs.
Either way, I've enjoyed the story and romance (chik side), although when I finally went D*K side, I was blown away by the story that was there too. It changed my impression of some of the characters, drastically.