Well, there are lots of things you could do to aircraft from the get-go to improve performance, considering the level of technological advancement and refinement that went into aircraft over the 1939-1945 period.
I'm a RAF fan and my personal favourite aircraft of the war is the Typhoon. If you take a whole lot of minor improvements that happened to the Typhoon airframe (new aerials, gun shrouds, tail wheel doors, internal mass balance, new propeller, new exhaust, internal rear view mirror) and add them all together, then you end up with an startling improvement in performance.
The Typhoon improved its level speed from about 390 mph at best altitude (~18,000 - 20,000 ft) to about 415 mph at the same alt on the same power over the course of three years of refinements. 25 mph for what are essentially minor modifications to the airframe is not bad. What if they had all been there from the start? What if the Camm had designed the Tempest II from the start, instead of progressing from the Typhoon
Suppose that a couple of things happened in the Typhoon design process:
1. Sir Sydney Camm ignores both the incorrect advice of the RAE about the effect of thick, Hurricane style wings on performance and RAF's concerns about the vulnerability of wing radiators and goes with thinner, better performing wings and no chin radiator (also putting a larger fuel tank in the fuselage). Result: Better speed and dive performance at the cost of a little range, although climb performance may of suffered (although it mostly depends on wing profile and size);
2. Napier goes to Bristol in 1940 instead of 1942 to sort out some of the kinks in the Sabre, meaning a reliable engine by 1941;
3. Napier has the necessary funding to develop a two speed, two stage supercharger for the Sabre, meaning a 2,000 hp + engine that delivers rated second stage power to about 22-23,000 feet, instead of about 15-16,000 feet;
4. Camm redesigns the rear fuselage to eliminate the problem of rudder flutter and sympathetic vibrations buckling the rear fuselage at the tail joint;
5. A larger, Tempest V/II style tail is fitted to deal with torque on takeoff;
6. The cockpit seals are redesigned, meaning that carbon dioxide and other nasty gasses don't flood into the cockpit;
7. Bubble canopy from the get-go (already somewhat present on the Whirlwind), improving visibility;
8. Spring tab ailerons fitted from the start, notably improving roll performance, always a Typhoon weak spot;
9. Four bladed prop fitted from the start, improving acceleration;
10. Gun-bays redesigned, allowing more ammunition to be carried (think it was about 20 more rounds per gun at the end of the war);
11. All the little improvements previously mentioned are already there
So, with all of the redesigns what do you get?
First of all you get better reliability and serviceability. Operational readiness, the Typhoons major bugbear in the first 12 months of operations, is radically improved. No to-ing and fro-ing with the RAF about whether its going to get cancelled or not. No welding fishplates to the rear fuselage. No erks standing by with a fire extinguisher on start-up for 18 months. Pilots don't have to continually wear oxygen masks in the aircraft.
Second, overall speed is significantly improved. The big difference comes from eliminating the thick draggy wings (a la Tempest) and the honking great chin radiator. I'm not going to put an estimate down on paper, but with the thick wind and chin rad, the Tyffie could still do 417 mph at 20,000 feet
Thirdly, high level performance is DRAMATICALLY improved. Thin wings and a two stage, two speed supercharger mean that the speed and climb of the Typhoon at higher altitudes (say, above 18,000 ft) is transformed. Maybe not in the same league as the later Spitfires, but at least as good as the Merlin 61 powered Mk IX up to 25-26,000 feet.
Fourthly, the Typhoon becomes a fighter. With more speed, more power at altitude and, very importantly, a better rate of roll (spring tab ailerons) the Typhoon gets turned back into an offensive, manuverable fighter, instead of a 400 mph brick that rolls like an elephant stuck in tar.
This means offensive Rhubarbs and Rodeos at 25,000 feet across Europe and right through the Northwestern German border. No stooging about at 12,000 feet over France, looking for ground targets while being subject to flak and being bounced by all and sundry. The Typhoon's range was about 175 miles better on internal fuel than that of a Spitfire IX and range with 2 x 45 gal drop tanks was bang on 1,000 miles. Guesstimate a combat range of 350 miles, maybe more with larger D/Ts. How about the image of Typhoons escorting Lancasters and Halifaxes to Essen and Dusselfdorf, or perhaps further?
Fifthly, and finally, the aircraft becomes available earlier than historically. With a reliable Sabre, no faffing around with the Tornado/Tempest/Fury line until later in the war, no changing RAF/RAE design requirements and no redesign of minor items, the Typhoon becomes available at least 4-6 months earlier than in the actual historical timeline. That means that the Spit V has some help on hand when the FW 190s start to really make their presence felt in late 1941.
Purely hypothetically, the RAF could of had an aircraft with similar (if not the same, or perhaps a little better at altitude) performance to the Tempest in mid-1941. Around 365-375 mph on the deck, 425-435 mph at 25,000 feet, 3,600 ft/min + rate of climb, good rate of roll (never great though) and 1,000 mile range.
You can repeat this whole process for the Spitfire as well. Maybe put in a 30 gal rear fueslage tank from the start, 20 mms properly installed, better fuselage skinning and panel design for reduced drag, new profile radiators, wheel well covers, rear wheel cover, wide track, forward raked landing gear, small forward wing tanks, metal skin ailerons, internal bullet proof windscreen, better tail/rudder design, revised elevator design, multi ejector stacks, more aerodynamic windscreen, fully sealing fuel tanks, larger capacity nose tanks, revised wing spar design, revised rudder balance, stronger control linkages, frise type ailerons, blown canopy ect, ect, ect