I honestly think the biggest problem with this adaptation is that it is, due to it's length constraints, overly simplified.
Pretty much every trace of nuance was lost from the games and the characters were all simplified to their most basic character traits and the plot was somewhat simplified as well.
The deaths in particular can be seen as the writer getting rid of characters that he/she simply doesn't know what to do with.
All in all it's still a perfectly average anime but it could have been great if they had been given more time.
I honestly think the biggest problem with this adaptation is that it is, due to it's length constraints, overly simplified. Pretty much every trace of nuance was lost from the games and the characters were all simplified to their most basic character traits and the plot was somewhat simplified as well. The deaths in particular can be seen as the writer getting rid of characters that he/she simply doesn't know what to do with.
All in all it's still a perfectly average anime but it could have been great if they had been given more time.