First let us look at the weapons.
The AIM-9s are more or less the same for both versions. If we consider that the Ls have been upgraded to M standard. Otherwise the M had a better seekerhead.
The AIM-7M however was comparable to the Sky Flash when it comes to the performance of the monopulse seekerhead. However it still was an AIM-7E when you look at the motor and the aerodynamics. The M featured a new warhead (focused blast fragmentation) and better range. So we have to give this to the F-4E.
Now look at the avionics. Some F-4E had TISEO and most USAF version had the very important combat tree asset. Also the RWR was better on late block F-4Es was better. And the cockpit layout + HUD (if you want to call it that way) was better in the E.
The radar hwoever is a more interesting topic. The F-4E APG-120 was credited with a range of roughly 100kms (on a good day), but did not allow to engage multiple targets, or to engage low flying targests from high alltitudes (look-down-shoot-down). The british AWG-12 however is known to have been acceptable when engaging low flying targets, while giving a comparable or better range. So this goes to the F-4M.
Now look at the airframe. The M was faster to accelrate, but slower and was temperature redlined at Mach 1.9 due to some cheap materials used in the engine. It was more economic in flight, but that was compensated for by the increased drag of the redesigned inlets. The Spey was also a lot less responsive then the J79-GE-17 on the F-4E. So this goes to the F-4E. Slatted variants added an advantage in dogfights.
Overall the F-4E was the slightly better aircraft. Or we should say that the F-M was the better aircraft for huntig soviet bombers over the North Sea and the Atlantic, while the F-4E was the better aircraft for use over the central european front.
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