The first and most important thing you need to understand about using the past perfect was expressed by FumbleFingers here.
The guiding principle should be don’t use Past Perfect unless you really have to.
The reason your friend found your sentences ‘busy’ is probably that the word before expresses everything you want the past perfect to express.
I met you before you met her. You could also express this as
I met you and then you met her.
The second thing to understand, about perfect constructions in general, is that a perfect construction does not narrate a prior event, it expresses a current state which exists as a consequence of the prior event. For instance:
We arrived at the cave, only to find that the mouth was blocked by six feet of sand. Luckily, I had packed a shovel, so we were able to clear an entrance.
That is, the past perfect expresses the fact that when you arrived you had a shovel in your possession, because earlier you had packed one. In cinematic terms, it's not a ‘flashback’, a jump backward in time, but a sort of temporal ‘pull out’—the ‘camera’ backs up so the field of vision brings the past into view, but it remains as it were focused on the point at which you discovered the sand.
Consequently, the past perfect should be used only when your narrative has defined a specific point in time (the technical term is Reference Time) at which the state established by the prior event becomes relevant. This is not the case with your two sentences:
I met you before you had met her. ... there is no Reference Time after their meeting to which the past perfect is related.
I had met you before you met her. ... This is closer to working, but it still does not define a time at which your earlier acquaintance became relevant. This might be established (and usually would be) by further context:
I met her—it was the first time the three of us were together—at that dinner at Spiro's. The two of you were just becoming a thing, but I had met you long before you met her, so you and I were more relaxed with each other. I think that bothered her, and is why she still resents me.
As a native speaker, I have to say that I would never use the second sentence, "Did you see what they had done to our city?", except to describe a state of the city that has passed. For instance, if someone had painted a wall, I would ask a friend, "Did you see what they have done to our wall?". If that paint was then washed off, the question would be "Did you see what they had done to our wall?" as that state of "painted" has passed.
As for the difference between sentences three and four, I do not see any. It's just as correct to say "Did you see what they have done to our city?" as it is to say "Have you seen what they have done to our city?". However, I would say that if you asked somebody returning from the city, you would say sentence three rather than sentence four, as "Did you see" implies that they could have seen as opposed to "Have you seen" which implies that they may not have had the chance yet.
For instance, if somebody went to a cinema the same day that a new film was showing, I'd ask "Did you see that film?". If we were talking about the film, and I didn't know that they'd been to a cinema, I'd ask "Have you seen that film?".
As for the fifth sentence, you're absolutely on point.
Best Answer
Either is fine, although the second is more concise, and at least equally clear, so I'd pick that one.
The past perfect (1st sentence) would be preferable when the events are out of order: