Especially in the Luftwaffe. Were the aircraft such pilots such as Hans Rudel, given superior rear guns in his JU-87 or armour to protect these more important airmen?
Speaking for the American air force, the aces flew the same aircraft as any other pilot did. When you add extra armor to a plane beyond its design specifications, it can reduce speed and maneuverability. In the case of Rudel's Stuka (which was already quite slow) doing this would impose a significant weight (and thus speed) penalty and could stress the airframe in a dive, making him more vulnerable to Soviet planes and even his own aircraft. The factor of speed is even more important when flying a fighter versus a dive bomber.
In many cases, pilots (not necessarily aces, but aces often did as well) modified their aircraft to make them more comfortable to use or to give an advantage over the enemy; the 56th Fighter Group diligently waxed all their P-47 Thunderbolts to make them slip more smoothly through the air. The P-47 Thunderbolt's factory-fitted rear view mirror was not the best design, and so some pilots replaced them with mirrors from Spitfires. "Bud" Mahurin did just that, and attached two more spare P-47 mirrors to his plane below the windscreen on each side of the cockpit to give him a better rearward view; other pilots in the 56th Fighter Group did this as well.
His P-47, like some others, also had the flat wheel hub covers removed at some point as presumably unnecessary. The 20th Fighter Group, after they converted from P-38s, took the mirrors off their old planes and put them on their new P-51 Mustangs.
When a fighter group was first constituted, each pilot had his own assigned plane. As the war wore on and casualties mounted, there were often more planes than pilots needed to fly them. This problem became more acute when fighter groups were authorized to expand from 75 to 108 aircraft in the winter of 1943-1944.
Pilots selected to fly a mission flew whatever aircraft was available that day, which sometimes would not necessarily be "their" aircraft. It was an unspoken rule in the Army Air Forces during the war that "new" (replacement) pilots weren't assigned their own plane until they had flown x number of missions or accumulated so many flying hours. Until then, they flew whatever aircraft was available.
Sources:
Zemke's Wolfpack: A Photographic Odyssey of the 56th Fighter Group During the Second World War, by Nigel Julian and Peter Randall
I can answer a bit for the Navy, especially early war (1941-1942).
Because the situation was that there were never enough Wildcats on carriers to go around every pilot in the squadron from the CO on down would rotate, usually by flight or at least division if they had to.
So a squadron might have 30 pilots, but only 26 planes to start the cruise, then a month later only have 22. So you are going to have to rotate planes. Each plane in the squadron would be numbered and theoretically assigned a pilot base don position (F1 being the CO's plane F2 his wingman, F3 the other element leader in his flight, down the line). But when you have some planes under repair, others spotted quickly out of order on the flight deck, changes in plans or mission rosters, it all got very jumbled.
That isnt to say that they didnt have favorite or preferred aircraft, perhaps for whatever reason one Wildcat had a more efficient turbocharger, or one kept losing oil pressure every so often and wasnt liked, but in the end there werent enough planes at the time to be picky.
And the F4F's flown early war (3, 3A, and 4) were all damn survivable aircraft that worked wonders to bring their pilots home to begin with.
Source. The First Team: Carrier Fighter Combat from Pearl Harbor to Midway by Lundstrum.
As the other commentators here have indicated, even ace pilots tended to fly a roster of different aircraft. The modifications to the planes tended to be done not in the factory, but at the local airfield. Such field modifications tended to be relatively minor and reflected what pilots perceived as necessary for combat. There were very few examples of "special" ace custom aircraft during the war, and such that existed were not so much for special pilots, but to test the potential for these modifications to be incorporated into future production lines. One example of this was Adolf Galland's three "special" Bf-109 F-2s. As commander of JG 26, Galland had three of its Friedrichs modified to carry a heavier armament. Two of the aircraft had their cowl MG 17s replaced with two 13 mm MG 131, while the third aircraft had a two 20 mm MG FFs in the wings. But Galland had his mechanics make these modifications not because he personally wanted an up-gunned fighter, but rather because he felt that the BF-109F was undergunned for the average pilot's skills. As Galland was making his ascent up the Luftwaffe's hierarchy, these modifications were a proof of concept rather than a perk given to an elite.
I can't remember his name, I think it was Alexander Pokryshkin, but there was a Soviet pilot who flew the lend lease planes and he made a modification to it. In the Bell P-39 Airacobra you could have 3 caliber weapons on the plane. Most common was a 37mm cannon in the propeller hub, 2x .50 caliber machine guns mounted in the nose cowling firing through the propeller, and 2x .30 caliber guns under the wing. There was a switch in the cockpit that could choose which gun to fire. This pilot ripped out the switch and wired it so that all his guns would fire at once. All that lead flying through the air you're bound to hit something, right?
In reference to your question, if planes of aces were modified specifically for them? No. Going with your example, Hans Rudel flew the Ju-87 and later perfected becoming a tank killer, first with bombs then with the G model armed with the 37mm cannons. The Stuka was a slow, stable platform for dive bombing. Because of its slow speed it needed the added "protection" of a rear gunner who could at most hope to scare away any attacking fighters let alone shoot one down. Hans Rudel did fly an FW-190 and achieved numerous kills in that, he even shot down soviet bombers that happened across his path in the Stuka, there was nothing that man wouldn't bomb or shoot.
Keeping with this German theme Erich Hartman, the ace of aces with 352 kills, the only notable modification he added to his Bf-109 was the a black tulip on the nose. This eventually identified him to soviet pilots who avoided combat with him. He then would give his wing man the "black tulip" aircraft so they would not be interfered with while he went on racking up kills against the soviets.
The pilots just flew the planes they were given and depended on their skill as pilots to see them through, no special or "superior" weapons, or armor were given to them. Hans-Joachim Marseille the top scoring ace in North Africa, acquired the majority if not all of his 158 kills against the British, flew over 10 different Bf-109s and was killed jumping from his aircraft a Bf-109F-4 when the engine started smoking. A number of pilots did not care for the F model that came to the desert complaining of the problems the engines were having with the elements present in North Africa.
Was the Bf-109 superior to other aircraft? At the start of the war yes, but by the end the only the K model could hold it's own against the newest fighters the allies had to offer. Why did the Bf-109 become the stable for the majority of the highest scoring aces? The majority of those high scoring aces achieved their kills on the Eastern Front against the hoards of aircraft the Soviets put up in the air piece meal. Of course there are exceptions notably the previous mentioned Marseille who scored all of his kills against western opponents. Just didn't want anybody thinking the Bf-109 was defacto the best fighter ever developed.
Douglas Bader, the RAF ace who lost his legs in 1932, flew a slightly unusual Spitfire. The first mark of the Spitfire carried eight .303 machine guns (in what became known as 'A' type wings), but from 1941 the vast majority carried two 20mm cannon and four machine guns ('B' wings). Bader had always opposed the cannon armament, so when the rest of his wing were equipped with the Spitfire VB, he insisted on flying a Spitfire VA; this wasn't completely unique to Bader, but there were less than 100 Mk VAs built compared to more than 3500 Mk VBs, so it was somewhat atypical. For the most part, though, as others have said, aces flew standard aircraft.