Okay, there seems to almost be two schools of thought on which are best Guards books.
There are some who think that the early ones--"Guards, Guards" and "Men at Arms" are the best of them.
Then there are some who think that the later ones--"The Fifth Elephant" and "Thud!" are the better ones.
I wish to posit a theory, open to refutation, that one's favoring of GG/MA over TFE/Thud (or the opposite) depends on whether you are primarily a Vimes fan or a Carrot fan.
In the first two books, Vimes was nothing like the Vimes of the later books. In GG he was drunk, powerless and (often) a stupid bumbling coward who totally cowtowed to Vetinari. If hadn't met Carrot and Sybil, he never would have amounted to anything. Carrot is pretty one-dimensional here, too, but you see his potential of emerging as a main character and eventually replacing Vimes.
In "Men at Arms," the story was nearly entirely Carrot's. He emerged from being a 'boy' to a very resourceful copper, while Vimes was in the background for most of it.
Pterry admitted that when he first started the series he thought the Carrot was going to be main Guard, but that Vimes just emerged as the more interesting character, and he gradually added layers to Vimes while diminishing Carrot's over time.
The 'Vimes' of the later books only began to emerge in "Feet of Clay," where we began to see that genuine 'copper' intelligence that had been in short supply in previous books. Carrot is still an important character, but Vimes is much more of the "commander" here.
By Jingo and TFE, Vimes has clearly become the main character of the series, and Carrot's role is far more of a right-hand person. In "Thud!" he serves as little more than a CSI investigator, and is nowhere near the climax of the book in Koom Valley.
If you like Vimes more than Carrot, you probably prefer the later books, where Vimes' personality ads layer upon layer, making him probably (along with Granny Weatherwax) the most fully rounded-out figure in the DW series.
If you like Carrot more than Vimes, you probably prefer the earlier books, which more closely reflect the 'comedy-driven' style of the earlier DW novels, and where Carrot is a far more dominant personality.
If you don't prefer one or the other, then you prefer books for whatever reason you prefer.
Me? I'm a Vimes man, through and through, which is TFE and Thud! are #1 and #3 on my 5 favorites DW books and GG wouldn't even make my top 10.
Thought? Refutations? Poohisms?