AP
So lets see Penthesilea is scaling somewhere above 385 megatons (that + technically means it doubles but thats just not fair) plus her ME stat boost. Diana is scaling from 545 megatons so Diana will have a small AP advantage.
Durability/Stamina
Neither are stone walls so they can harm each other. Stamina however goes to Berserker. Not only does she have better regen (not that much better but it helps), she would be comparable to other Servants who can fight for days. The only thing we know about Diana's is that she can fight for more than a few hours (has she or supes ever been tired out?).
Versatility
Diana has her sword, shield, lasso and braclets. Berserker has spiked armor, spiked ball, spiked chains and a pair of swords. Given that both default to cqc the chains and lasso probably wont see much use.
Skill/Intelligence
Penthesilea is more skilled seeing as she was able to take on
Achilles without instantly dying and survived for a while (Achilles is second in skill to a sane
Heracles who easily outskills (a weakened)
King Arthur while insane. Achilles is called equal to
Karna who hits harder because "muh skillz", proven by the fact both of them can tag
Siegfried without getting tagged and only failed to kill him because invulnerability. Siegfried also stomps
Mordred and is equal to
Lancelot who also completely outskills King Arthur.)
All that means nothing though (shouldn't have even bothered typing) because EX-ranked ME, HotWG and Diana in general makes her insane, so Diana has the advantage in skill. HotWG does screw with Diana's mind though so she isn't fighting with full skill.
Conclusion
Normally I'd hand it to Diana at this point since with speed equalized she has both skill and AP but ME makes the psycho even faster which should make them evenly matched (plus have you seen how "unskilled" insanity makes Servants). Long fight (probably) but Penthesilea goes for her Outrage Amazon sooner or later which makes her hit even harder and more berserk. Even if she survived OA, I see Diana getting worn down and losing.
Notes
I would have brought up TK and flight but Diana has only used the former on projectiles and the latter just isn't used for some reason. If she did, flight + lasso = GG.