Diplomacy is broken

[diotavelli]

So I think I proved my point: these states didn't survive the war with HRE (thrice their lands) because of the fact little ones always have chances against a big one, but because of the low arrangement of the HRE in that times which made organizing a full war hard for it; if the HRE was at that times able to retaliate, I who am from Bologna might speak German now.

No, I think you're wrong. The HRE frequently conquered northern Italian cities. IIRC, Milan was destroyed on at least one occasion. It is not the case that all these little states survived because they weren't beaten but that they survived because, having been beaten, they still had a sufficient sense of independence to reassert themselves when they had the opportunity. On the other hand, on some occasions, the little states did successfully stand up to the HRE (e.g., the creation of Alessandria).

About Scotland, it was conquered, but not in times of a MTW2 game; not in 15 turns!

Yes, but you ignore my other example: Wales. Llewellyn ap Gruffydd struck for independence in the reign of Henry III but Gwynedd was conquered early in the reign of Edward I. In game terms, this is around 15 turns.

The fact Scotland resisted invasion for so long shows how they had an army not so 1/3 of the English's. Or were all the English generals incompetent for centuries?

Scotland didn't successfully resist throughout the "5 centuries or more" you mention earlier. There were frequently English garrisons in Scottish castles in this period. Berwick-Upon-Tweed was lost. The Scottish recognised more than one English king as their overlord.

The fact that Scotland wasn't completely subjugated by the English is not because their military strength was greater than 1/3 but because they were fighting on one front and England wasn't. England had to contend with France, troubles in Ireland, Crusades, internal revolts and civil wars and so on. None of this deflects from the fact that English power was far, far greater than that of Scotland.

And a lot of English generals were incompetent - much to the satisfaction of my ancestors, who remained proudly Irish throughout.

All of which is beside the point of the game. In MTW, factions could respawn to reflect that, whilst the military forces could be defeated, nationalist sentiment was far harder to destroy. M2TW doesn't have this feature, so factions can be eliminated comprehensively.

So there we go: M2TW is accurate in allowing England to conquer Scotland in 15 turns; it is inaccurate in not allowing the Scots to reclaim their independence when they'd spent enough time living in bogs watching spiders.