Yeah, the thought of the rose being a boss battle has crossed my mind. It's weird, but considering how many random filler bosses there are in this game, being able to fight something that you know you have to destroy would gave been interesting. And it would be fitting, with all of the plant themed enemies in Scarleticia and its overworld area. You go into Sonya and Neclord's dungeon expecting to fight them, and Kwanda's black rune only melts once you beat him in a duel, so it just feels a little anticlimactic that Milich gets freed from the black rune without a fight and the poisonous rose is destroyed so easily.
And yeah, I always noticed that female soldier as well, and given that unique sprites aren't very common in this game at all, it would have been cool if she was made into a minor antagonist. It would be fun since all of the female antagonists in Suikoden I can think of (Sonya, Lucia, Sarah, Alenia, and Sialeeds) have some type of great personal stake, which motivates their opposition to the heroes, while for her it could just be that she's loyal to her country. Haha I know its just wishful thinking at this point, but considering I've played AOE 2, where fan-made mods and expansions have actually become official expansions, it's fun to think about what changes we would make.