Mid war 109s suffered from aerodynamic point of view as well. Simply from middle 42 to early 44, 109 received not one significant improvement in any way, engine or airframe or controls.
In WW1 germany also lacked competitive high power engines but still ,by excellent work in airframes and wings , created aircrafts fully equal (if not superior ) to the alleid fighters and pilot friendly (Fokker DVII , DVIII, Siemens DIV) .But in DVII case, it was MvR who had the final word how should be build. In WW2 aircraft programs was a chaos between Udet, Milch, RLM , Goring, aircraft companies, Hitler, political friends etc...Somewhre among them was the General der Jagdflieger but without any important impact.
I dont know if the Spitfire was overall better but certainly had a more orthodox and logical evolution
The Me 109G1 and G2 weren't too bad from an aerodynamic point of view, they didn't have the gun bulges yet and retained the retractable tail wheel and such refined aerodynamic features which came across from the Me 109F however with the DB605A engine restricted to 1.3 ata (about 1350 metric hp) the Me 109 was significantly behined the Merlin 61, Merlin 66 and Merlin 70 that equiped contemporary Spitfire IX's and VIII and offered up 1500-1720hp at a higher altitude.
From the Me 109G2 onwards all sorts of aerodynamic degradations progressively appeared in the G3, G4m G5, G6: cowling bulges when the 13.2mm guns replaced the 7.62's, wing bulges when the main wheels were enlarged, loss of the retractable tail wheel when it was enlarged, larger more draggy aerials.
The result is that the speed from 400.5mph for and Me 109G1 to 387mph for an Me 109G6. Speed of the Me 109G-6 went back up to 397mph in the second half of 1943 when the engine was rated to 1.42ata boost after faltering attempts.
Had The Me 109G6 retained a retractable tail wheel and had the gun bulges been engineered to be smooth (as was possible and even flight evaluated) the Me 109G6 probably would have made 397mph at 1.3 ata and 410 at 1.42 ata or thereabouts.
Had the engine produced 1.42ata from the begining it also clearly would have been much better.
It's hard to blame German engine manufacturers given the fuel they had to use and if the DB601A1a vs DB601N is a worthwhile comparison then about 10% more power could be extracted from the early 96/115 grade C3 fuel as opposed the 87 grade B4. The BMW 801 did rather well so its not quite right to say they had no good engines.
To me it seems compromising the the airframe (gun bulges, loss of retractable tail wheel) as opposed to actually improving let alone maintaining aerodynamic qualities was a mistake. It would have been worth waiting a few months longer for a proper solution.
By accepting compromised solutions tooling and parts promulgated throughout the manufacturing system and became even harder to achieve a proper modification.
Contemporary Spitfires had 10-20mph more speed and 10%-15% more power being able to sustain 408mph , this even after the DB605A1a had been released to 1.42 ata.
Engine power didn't improved till the DB605AM of March 1944 which offered around 1700hp, aerodynamic improvements came at the same time, but only on the versions with the enlarged supercharger of the DB605ASM which offered the same power but at higher altitudes. This is when the Me 109 restored its competiveness but it still wasn't enough as the new engines still went into airframes with the same drag issues and much potential was wasted.
I think this came at a considerable cost in pilot attrition.