I agree whole-heartedly.
Battlestar Galactica (I wonder how familiar with it you are) is a perfect mainstream example of effortless vs. effort-ful theme-dropping. S3 has an amazing mini-arc (New Caprica) that explores themes of colonialism, terrorism, guerrilla warfare, civil liberties, basically everything under the Sun... but it does this by focusing on a twisting plot and characters whose motivations we've come to care about, not by going on irrelevant rants about "meaningful" and "significant" ideas. When Colonel Tigh condones terrorism and even killing innocent civilians it's not because of some deeply thought out philosophy, it's because
he frakking hates Baltar's guts, and even if the viewer doesn't agree at least he can understand.
Which is a perfect contrast with the latter half of S4, which crams "deep" ideas about religion and destiny and coming-togetherness down the viewer's gullets at the EXPENSE of the characters. The characters become walking, talking mouth-pieces, the plot suffers, and the ideas feel hollow and unnatural.
You're spot on here. There's nothing wrong about Metzen's interpretation of the Raynor/Kerrigan romance, the only problem is when that is allowed to become the only driving question in the story.
Why is that allowed to become the driving question? Because the plot is one-dimensional enough to allow that to happen. If more complicated plot elements were introduced through peripheral characters (Mengsk, Valerian, Tosh, new characters), if the struggle for goodness and justice became less black-and-white (in the final game, it turns out that the choice Raynor makes is the ONLY correct choice; the only conflict was whether he was going to continue wallowing in self-pity or not), their romance would naturally have been pushed to its appropriate place. Which isn't to say that that place wouldn't have included a cinematic at the very end of the game just like what we got... maybe it would have... but that cinematic would have been tempered by everything that had come before.