Telling two equally successful tales within the same time frame is a structural challenge. As Jacob Krueger explains, while examining Blue Valentine and Dead Poets Society, ratcheting up the tension between parallel stories will help raise the stakes for the characters, and raise the interest of the viewer.
Your job is to determine your show's over-arching architecture and be able to articulate it, both in a verbal pitch and in the design of your pilot. The good news is, there is no shortage of good model structures on the air as we speak.
The protagonist is really on three journeys: the “A” story — the plot; the “B” story — the relationship; and the “C” story — the internal journey dealing with [a] flaw. These journeys are intertwined and interdependent. Often, a plot point for the A story serves as the same point in the B or...
Don't blame writers for a dearth of originality. They're busy writing, developing, and pitching the most creative, engaging stories they can... but they don't get to decide whether those stories get made.
Don't break stories to reflect your theme. If you're lucky, and if you've written solid stories, a theme will start to emerge.