There is advantages and disadvantages to everything. Look at this:
There is a clear advantage to this: It makes the beat very easily recognizable. It has some clear disadvantages: The rhythm is rather hard to read.
Compare this to this:
Here the beat is less clear (although still quite clearly indicated by the bass line), but the rhythm of the melody line is very clear.
There is a common compromise, which is to break and tie notes hanging over the middle of the measure like this:
which is less confusing wrt. to beat compared to version 2 and easier to read wrt. rhythm than version 1. So this often is a nicely working compromise.
In the end the main objective of notation is to be readable. And the best way to achieve this depends very much on context such as the type of music, what the musician that is supposed to play it would be used to, the setting where the music is to be performed in (is there need to be extremely precise with the metrum?) and a lot more. So there is no universal way to say “this is how it should be done”. It is an editors job to find the best version for the edition he is doing.
Especially with more complex piano music you’d often find that things are done in a way to make the different melodic lines easily understandable, not necessarily following the meter strictly. With orchestral and big ensemble music you tend to get more notation aligned to the meter, since it really matters that things are aligned (also having just one line makes it harder to get the meter).
