The Ju-88G1 had a top speed of 565 Km/h as opposed to 540 Km/h for the Pe-3bis. It also featured 6 20mm MG151/20 and radar as opposed to a mix of 2x 20mm, 2LMG and 3 BMG of the Pe-3, of course without radar.
The Pe-2/3 does not compare favourably with the Bf-110c/f/g in terms of firepower, speed, acceleration, range and bombload and less so with the Mossie. The Ju-88 is slower in the bomber version (Ju-88A) but faster in the recon version (Ju-88S) as well as in the later nightfighter versions (Ju-88G). I am not sure that the Pe-2/-3 are more maneuverable, from what I read all Junkers aircraft had very light controll forces and were more maneuverable than the size of the airframe would imply.
The Pe-2 is a decent all arounder but the Tu-2 is the better bomber plane and unlike the Mossie / bf-110 / Ju-88 it was never a successfull nightfighter.
I also have problems with the Pe-2 performances. Top speed was typically 530 to 540 Km/h for all operationally used variantes, except for the late 1943 Pe-2FT which claimed 580 Km/h instead of 540 Km/h with VK-105PF instead of VK-105.
I doubt that You can achieve 7% more speed with just 7% more power aviable on the same airframe. The speed does not increase linearely with power. It does increase with the cube of power. Note that the -105PF was a M-105 modification with increased SL power output at the expense of decreased high-altitude performance, which in turn makes the claimed 580 Km/h even less believable. Still in within the range of speed differences for individual planes but suspect when used for general performances.
The Pe-2I was produced in five specimen before the end of the war (trials in mid 44) and should be compared with the contemporary Ju-388.
Pe-2FT by V.M.Petlyakov