There was actually a higher combined troop total at Waterloo then Gettysburg, but Gettysburg had considerably higher total in artillery.
The artillery casualties at Waterloo (where all pieces were smoothbore) were largely a result of the high troop density on the battlefield, in fact the largest troop density in the whole of the Napoleonic Wars - over 24,000 men per mile.
The question why the Confederates stuck with 4 gun batteries is a good one and is difficult to answer. First point to make is the logistical problems caused by mixed types in a single battery and although individual pieces would have their own limber and caisson with ammunition for that particular piece, resupplying the battery after firing was the major problem. Up until Antietam the Confederates still made use of 6 pounder smoothbores even though they were obsolete as there was little else. Many of these cannon were left behind in the advance into Maryland in 1862.
For example look at S.D. Lee's battalion at Antietam consisted of the following batteries on the artillery line:
Bedford (Virginia) Artillery, Jordan’s Battery: Capt. Tyler Calhoun Jordan
1 x 3” Rifle, 1 x 10pdr Parrott, 1 x 12pdr Howitzer, 1 x 6pdr SB
Richmond (Virginia) Artillery, Parker’s Battery: Capt. William Watts Parker
2 x 3” Rifles, 2 x 12pdr Howitzers
Brooks' (S. C.) Artillery, Elliott’s Battery: Lt. William Elliot
2 x 10pdr Parrott, 2 x 12pdr Howitzers
Ashland (Virginia) Artillery, Woolfolk’s Battery: Capt. Pichegru Woolfolk Jr. (4 x mixed guns, vet)
2 x 10pdr Parrotts, 1 x 12pdr Howitzer (iron), 1 x 6pdr SB
The 6pdr was temporarily attached from Fleet’s (Middlesex) Virginia battery
Apart from the logistical problems, ranged against this line of artillery were Hunt's 'guns of position' stationed on the far side of Antietam Creek with interestingly at least four 4-gun batteries of 20pdr Parrott Rifles - Wever's, Kleiser's, Langner's and Taft's batteries. So in terms of counter battery fire it was largely one way traffic.
The Confederates were largely dependent on captured pieces for their higher calibre artillery at this stage of the war, for example 2 x 20pdr Parrott Rifles captured at Harper’s Ferry were issued to Elliott’s battery replacing the Howitzers after Antietam.
But perhaps the largest problem the Confederacy faced was the lack of potassium nitrate, the key ingredient of gunpowder. At the time of the civil war the sole supply was from British India and with the blockade this was out of reach for the duration of the war. In fact it was not until Spring 1862 that the Confederate Government out of pure necessity instituted a large scale nitrate program.
First were low grade deposits found in Kentucky and Tennessee but these places fell to Federal forces in early 1862 yet even with these deposits, the Confederacy was only producing under 500 pounds per day. Therefore a large scale search for suitable deposits was undertaken and were found in Texas. This was supplemented by further imports from Mexico and so production was able to be increased to around 2,000 pounds per day. Without this systematic search and discovery by Major I.M. St. John of the Nitre Corps the Confederacy would not have been able to continue as long as it did.
So largely the 4 gun battery was out of necessity with the continual lack of gunpowder, properly formed ammunition and suitably trained manpower all being limiting factors on the total amount of artillery available. As artillery was seen as supportive to the infantry as artillery batteries were attached to individual brigades, it was seen as better to have 6 brigades being supported by 4-gun batteries rather than only 4 brigades supported by 6-gun batteries. It was easier to combine these 4-gun batteries into an artillery firing line rather than having to split 6-gun batteries if that situation arose.