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There have been several advancements to be honest. The environment is now fully 3D, and 3D cutscenes (rendered) are now in place. Sure, this game was lacking a little bit. But that's because it's something new, well a new formula that Vos is trying out.

I think you have to relay everything. But start from Day 4, since that day onwards affects the ending.

No, the red section is when you become the alien-human hybrid. The green section represents when you were still a human-cyborg, I guess.

Fight the boss again.

Oops, I missed one instruction.

After you transform into a mutant after taking a final dose of DNA, you have to go back to the Quarters where your cybernetic leg was (this was where Geminis broke your drone). Then, interact with it and get the override chip.

Then after that, the "Help...Ka..." message will appear.

As an addition to what OdinLin says, when you run back to the generator, click on it, and select the "Charge" option, then RUN on back to the boss.

You can change your choices based on scene selection. That's what I've been doing.

This is not a bug. It is a recording, it even says "Playback" on the lower left hand corner.

Don't do any of the things I mentioned above.

Yes.

To get the 75% ending:

-Say yes to all yes/no prompts.

-Hack the CAOS ship in the hangar. (To do this, access the menu in the bridge and choose "remove locks" after using a bio-explosion to blast the door off. 

-Grab the data disk when priming up the gate in the control room.

To get the 100% ending:

Edit: Make sure you also collect the override chip from your cyborg leg after transformation into a alien-human hybrid.

-Do everything above.

-This time, when you receive the message "Help..Ka.." after the boss battle, go back to the area where you killed the monster with the machete. Then, interact with it, and continue the game as usual. You will unlock the last ending.

Yeah, you definitely need to check yourself, bud. His first publicly released game, "Xenotake" actually shaped the (especially Western) H-Game market significantly. If you haven't heard of Vosmug, you are more or less likely living under a rock. That too, is an understatement.