Other Episodes
We know the synopsis for the first thirteen episodes of Phase II, and while the majority of them would have been fine, a particular two-part episode called Kitumba would have drastically changed some elements of modern Star Trek. In addition to the pilot itself, you'll recognise two other episodes because they later re-used them for episodes of Star Trek: The Next Generation.
Tomorrow and the Stars
This was a bit of a mish-mash of Original Series ideas. Basically a transporter accident result in Kirk ending up in Pearl Harbour shortly before the Japanese Attack. He falls in love with a married woman, and realises that he can't warn anyone because of the drastic consequences it would have for the Second World War.
The Child
This is the first of our Star Trek: The Next Generation double bill. This one didn't change a great deal, with Troi taking on the Ilia role. The main reason why it's pretty much the same as the Phase II version is because at the time there was a writer's strike on and so they were unable to re-write it. The story was originally pitched by Jaron Summers, but it was Jon Povill who later took on the idea and redeveloped it. In fact the only significant difference other than the crew and the vessel, was that the alien which possessed Ilia was in part of a development life cycle that required the process rather than simply being an inquisitive alien.
Cassandra
A story by Theodore Stugeon, writer of Original Series episodes Amok Time and Shore Leave. It was intended to be a comedy episode. Basically think clumsy Yeoman and a cute cuddly animal. Hijinks! Hijinks!
Practice in Waking
This is essentially a holodeck story before they thought up a holodeck. But replace the holodeck with "directed dreaming" where the same dream is shared by multiple crew members and those crew members get stuck and forget that they're dreaming.
Deadlock
A story of mind control, testing on crew members and the changing of the perceptions of reality. Apparently all perpetrated by Starfleet on its own crew. Or is it?