Concerning historical events and scripts: Sounds to me like the approach GWX went, and I was MORE then just happy with that.
The users actions have impact on the overall actions of the Allies, yet major historical events (Op. Weserübung, Dunkirk) will appear and to a certain extend hold the lines of WW2. Sounds reasonable to me.
Concerning damage system: Has been modded several times already and I am willing to bet my last torpedo that it will be among the moddable aspects of SH5 as well. I do however applaud that they at least go in the direction of flood-sinking and let us hope that hp-kills will be (at least to a certain extend) made less attractive.
Concerning 3D deformation: In the old days, when SH5 was still only a dot on the horizon, there were promises that you could even shred the bow off a destroyer and she might limp on. (Looky here:
http://en.wikipedia.org/wiki/HMS_Eskimo_(F75)) Sounds promising to me. If it is actually in the game ...