I am not against any feedback, but you should understand, that you have one view and I have another view:
From the title, this looks like a feedback thread and I'm giving feedback.
1)You view (correct if not right):
*this is bad to break compatible with YR 1.001
*NPatch should looks like YR 1.001
*NPatch should use GAMEMD.EXE
*this isn't bad to break compatible - it open a lot of new features
*NPatch can have my small additional to game.
*NPatch should use new name, this will avoid a lot of problems.
Both sides have good arguments IMO.
people will install NPatch SE for mod and if mod designed for NPSE, it can turn off new menu.
The menu system doesn't even stay consistent, it just changes after that first screen. People will blame the patch for being buggy when really its just that the defaults for some tags will be set (from the point of view of unmodded YR) wrongly. This wouldn't be a problem if it was combined with UMP to make an unofficial patch that fixed bugs as well as settings the tags correctly for default behaviour, but it isn't.
I will remove this menu from NPAE, instead NPAE will be released with my small campaign (which demonstrate AlternateMap stuffs)