This is a great game even though it might seem a bit complicated and overwhelming at first. One thing to remember about the collectibles is the fact that you must
finish the entire run through of the game to be able to get them to carry over. I say this because achivements will appear as soon as you finish certain things but that does not make the collectibles themselves stay put if you simply restart the game. You do not however need to get the A grade finish to be able to keep collectibles. Any ending will do, and there are several.
I don't want to tell you to much about the story in this game but in order to get the A level ending
you should focus on the main objectives at all times. Usually the game will get you to reload if you let a crucial mission time out but some of them will trigger an alternative ending which will not be the A level one.
Oh, and if you want me to grade this game in a scale of 1-10 I would give it a 8.5 or maybe even a 9.
Good luck with everything!
EDIT: Well YUNDER
beat me to it but if you read both of our answers you will hopefully get all the information you need.