I actually never liked Mitsuki just based on principal alone as a female, who went through the situation of liking the same guy as my best friend. Finding out the alternate route just made it worse for me.
I only base my opinions on the anime, not the game (as I haven't played it). I like both girls after all.
Oh and I was visiting the blog of one of my favorite doujinkas (he/she's never disappointed me before), and she wrote her thoughts/impressions on the light novel. Perhaps it is different from the opinions on Amazon, and it might have some useful information. In any case, here it is if you wanna take a look at it.
Spoiler for Japanese text: