1. Don't confuse "story", "plot" and "structure". Sure, they're connected, and all books need a basic storyline, but there are different ways of letting the plot unfold. Sometimes, for instance in crime or spy fiction, the reader is often intended to feel confused: the entire story is revealed in the last few pages. Some stories start from the finishing point and describe how the central character got there. If the structure doesn't work for you personally, then say so, but that doesn't mean it's wrong.
2. Don't assume a central character has to be credible or likeable. The flawed anti-hero can do daft things, and can even be a pretty daft person: the concept of a little Belgian with a waxed moustache mincing around solving crimes is fairly incredible – but it works. The reader has to find the central character engaging, but that's not the same thing at all. What fails to engage you might engage other readers.
3. Don't get too hung up on background detail. A book can have too much or too little, or the detail can be wrong, but all of these can be corrected in edits or re-writes. It's the story that matters.
4. Don't "read a book by numbers" – with a check-list of things to write about. A novel is a work of art, and it deserves to be viewed as a complete entity. If you're struggling for something to write about in your feedback, then fine, a checklist can act as a useful prompt, but that's about it.
5. Finally, please never, never, never tell an author that their book is not fit for public consumption. Not in any way at all. The book might "not be for you", or "not to your taste", or even "not be a good fit for your publishing house", but you should always leave the author encouraged to write more – either to adapt the existing manuscript, or to write something else then return to that manuscript. Telling the author that they can't write or that the submitted manuscript is a 'bad book' is actually the height of arrogance – what special skills do you have to make that judgement?
Remember – that manuscript baby is likely to be the result of many long nights' hard work, perhaps years if it's a first novel. How would you feel if someone told you that your first-born was so ugly it was fit for the bin?