I just spent some time browsing through this thread in search of any reply that was against the integration of Kerbal Alarm Clock. I couldn't find any. KAC is developed by David Tregoning (a.k.a. TriggerAu), one of the Lead Programmers, so proper integration should be possible.
I honestly don't see why it isn't being integrated after it has been recommended in the first post that startet this thread and there is only positive feedback (as far as I could tell).
Has TriggerAu written anything about the matter?
I would love to see KAC added to stock. For me it makes me feel in charge of a real busy space program.
I like TheFrizz's idea (see below) of only making it available after some upgrades to the KSC, most importantly the Tracking station, but maybe also Mission Control (quest giver).
I could imagine that the functionalities would become available in tiers. At first you could only set raw time alarms, then maneuver node alarms, and only later the transfer peroid* planner would become available. There should of course be the option in the settings to just have it function, like it does now, so that stock and mod version don't need to be split.
* I know that most people call it transfer window, but the transfer window is technically the span of time each day when you can directly launch from a rotating body.
The launch period depends on the phase angle between your departure celestial body and your destination with regard to the central object both bodies orbit (e.g. the Sun / Kerbol).
Many launch windows may occur during a launch period. (For example: A launch period might be three weeks in July and the launch window might be from 3 p.m. to 4 p.m. every day.)
Just so I – newbie – have also added my 0.02$:
I don't think that KER and especially MJ should be added to stock. I'm sure they are great in what the do, but especially new players shouldn't be overloaded with information and automation should definitely not be an easy option within the base game. Once you are an expert, sure, go out, grab the mods!