I can name a lot more than three choices. How you handle the encounter with your cousin on Mhen'ga and Tarkus. How to handle the encounter with the sexbot AI and what to do with the AI core. How you handle Nova...
That said, while I can agree to some extent that some fights can be difficult if you walk into them unprepared... you can say that about the whole game. If you rush through and don't bother leveling up much and getting better equipment, you could pretty easily end up in a situation where you're screwed unless you have an earlier save to fall back on. A recent thread about someone stuck in Anno's mission comes to mind.
As long as someone is keeping the wiki reasonably up to date, I don't really think there's a problem here, difficulty-wise. Again, however, I would really like to have more inventory space - just take off the last slot of inventory and have it be a button that cycles between two pages of inventory slots.
A much more valid balance complaint: During the fight with the engineer in Karaquest 2, the number of drones she has can be 2, 3, or 4 - at random. That's kind of a big difference when you consider that any of them can blind you, and they all get an attack each turn. If I weren't already a wrecking ball with genitals at this point, I would be quite tempted to save-scum until I encountered her with only 2 drones.
Unrelated: What is the point of putting Kara in the radio tower during Karaquest 2? She says she can snipe people from up there, but she doesn't seem to actually do that, ever. I didn't see any combat damage from her in any of the fights I got into outside, or in the barracks.