Having watched the anime, I also felt pretty low for leaving Makoto at the shopping center when I wasn't playing her route...
yeah I had the same thing going on me.
Although I have to say I felt like I just killed 3000 nekomimi's by doing so.
I always have problems playing the bad guy in choice RPG games like KOTOR and Fable and the likes.
ME is an exception since I don't feel bad at all, the stakes are too high, the only thing that I never changed, or I had serious problem in that game was skipping on Tali Romance Plot... that was very difficult, luckily I have 3 chars, 1 Soldier (For Ashley) 1 Infiltrator (For Tali since I knew she will be romantic plot character in ME2) and 1 female Soldier (All purpose Renegade/Single/very cute too)
In Kotor the hardest Decision was when i waned to be dark revan was basically you could lead the entire game as a good Jedi, and at the end become a Sith Lord, but playing the game as a Sith Lord entirely was tiresome, but Juhani was a lot of help

In Kotor2 it wasn't so easy though, had to reload often before decisions cuz sometimes even selecting the bad choice could end up with Light Force influence

At that time being a Male protagonist is a hassle because of that white chick, and the other "sensitive" one that Hunger sent, but winning her over was worth everything
