When reviewing a manuscript for the second time, is it fair to comment on aspects I did not realise the first time? I refereed a manuscript and recommended a major revision.  Now, almost three years (!) later, the manuscript has come back to my desk.  The editor told me to treat it as a revision and not as a new submission.  However, since I don't remember the details, I'm re-reading the entire manuscript.

I'm noticing things that I consider need to be improved.  That includes things that were identical three years ago, but that neither me nor the other referees commented on.  There could be several reasons why I didn't comment on it the first time: 


I had less knowledge and experience than I have now, or 
the field has moved on since it's been so long, or 
I simply didn't notice something I noticed now.  


Is it fair to comment on it now, or did I lose my chance to suggest this improvement when I didn't suggest it in the first round?

On the one hand: I genuinely believe this needs to be improved.

On the other hand: if I were submitting a revised manuscript, I would not expect referees to comment on things they should have commented on the first time.  If nobody comments on a particular paragraph, I would assume all approve.
I believe that it is entirely reasonable to make major requests of a manuscript on second review, as long as it is maintaining your basic standard for acceptance rather than moving the goalposts.

For example, I have had the experience where things about a paper were very unclear to me in the initial review because of shortcomings in the authors' presentation.  Upon revision, those things became much clearer---but not in a good way.  The extra information shed light on serious flaws in the authors' work, which has led me to in some cases recommend further major revision and in other cases recommend rejection.

On the other hand, some reviewers seem to like asking authors to do entirely new work, not because it is necessary for publication, but because the reviewer wants to know the answer or thinks it will make "a more interesting paper."  This happens most frequently with "glamour" journals.  I believe this sort of "moving the goalposts" on publication is not appropriate even in the first review, and doubly so in a revision review.