Yeah, "Sins of the Father" does seem somewhat random. I don't get it. Maybe they just wanted to do a Klingon episode and didn't want it to be too far into the timeline (in other words, carrying lots of baggage) but they didn't want it to be "Heart of Glory", either.
"The Inner Light" is a perfectly reasonable choice. It's also my favorite of the episodes listed (as I'd imagine it is for most) but I don't like it quite as much as the majority of my fellow fans.
Yeah, good point on the pilot, too.