Jumping in - it’s been a few years since university, but let’s see what I remember.
Quick answer - at the time standard tuning became standard (late 18th/early 19th century), parallel motion of entire chords was not considered acceptable. The standard tuning provided greater flexibility of contrary motion between bass notes and upper voices, and also provided a variety of left hand fingering positions for the same pitches/chords depending on which strings were played. These advantages were very important to early guitar composers anxious to establish the guitar as a serious instrument, and therefore the E-A-D-G-B-E tuning came to predominate.
In greater detail -GEEK WARNING! The modern guitar evolved out of its earlier cousins - the lute, the vihuela, and the baroque guitar. Lute and vihuela tended to be tuned to something like G-C-F-A-D-G, with the possibility of extra bass strings. You can see that that’s the equivalent of dropping the third string to an F# and capoing at the third fret, which is what lots of people do when they perform renaissance lute music on the guitar. Baroque guitar often had doubled strings (‘courses’ is the term - a five course instrument would often have five pairs of strings tuned either in octaves or in unison.) and while there was no standardization, they were often tuned A-D-G-B-E.
Comes the late 18th century, and the six string guitar comes into being. While various other tunings were experimented with, the one that comes to predominate is the one we now consider standard. Why? Well, it has advantages - in the key of A, you have the open A, D and E strings available as bass notes. In the key of D, you have the open D, G and A strings available to use as bass notes, plus the G fingered on the 6th string at the third fret. Of the 24 keys (every chromatic note, ignoring enharmonic equivalents, factoring major and minor gives you 12x2), only 10 (C#, Eb, F, Ab, Bb, major and minor) have no roots of I, IV or V available as open strings. 4 (C, F#, major and minor) have 1 open string root for one of those chords, 4 (G, B, major and minor) have 2 and 6 (D, E and A, major and minor) have all three chords (I, IV, V) with available open string roots. So, we have an instrument which is not as versatile as the piano in terms of being able to play in all the keys, but which is more versatile than an open tuning, particularly in an age when sliding all the notes of a chord in the same direction (parallel motion, particularly parallel octaves and parallel fifths) was a massive aesthetic no-no. It took Debussy on the classical front, and a gradual acceptance of the worth of folk forms in popular music, to change this aesthetic by the end of the 19th century/beginning of the 20th.
I want to touch on one other aspect of standard tuning. Consider the first position E, A and D chords. [My convention - (#) = string number, # = fret.] The relationship of these notes of E (6)-0, (5)-2, (4)-2, (3)-1 is the same as the relationship of these notes of A (5)-0, (4)-2, (3)-2, (2)-2 and as these notes of D (4)-0, (3)-2, (2)-3, (1)-2. They are all (lowest note to highest note) the root, fifth, root up the octave and the third of their respective chords.
Now, take that D (4)-0, (3)-2, (2)-3, (1)-2. If you finger the following (no barres required!) - (5)-5, (4)-7, (3)-7, (2)-7 you will get the same pitches as the first position D. Different strings, different finger shape, slightly different tone colour. Now finger this - (6)-10, (5)-12, (4)-12, (3)-11. Same pitches, different strings, different finger shape. By now, you’re either regretting you brought this up in conversation, you’ve heard all this before, or your mind is blown.
This difference in shapes is the key to playing the guitar at the intermediate and advanced levels. It all boils down to this - if you find a block fingering shape (a chord shape, a grip, a LH position, whatever you want to call it - they’re all different names for the same idea) difficult where you are playing it, try taking it over a set of strings, or over two sets of strings. Look for potential open strings in the new position - did anything get easier? Maybe that’s the placement the composer intended.
It’s a little like piano, in that with the patterning of two black keys, then three black keys, the fingering of scales changes. C, D, E, G, A and B Major all finger the same in the right hand. C, D, E, F, G and A Major all finger the same in the left hand. The principle of sorting out the fingering of scale passages on, well, any keyboard instrument, is to figure out where thumb and third have to cross, and where thumb and fourth have to cross. For people like me, who came to piano in my 40s, that’s the hardest part about keeping my 88s straight, and that’s why I have so much work to do over Mozart, Haydn, Clementi, Kuhlau, Beethoven. Compared to those guys, I find the contemporary and Jazz rep way easier.
I hope this helps - brevity is a virtue and I am a wicked man.