Cells are extremely crowded and busy... and random and violent places.
Molecular biology dances in a nano moshpit from hell.
The Inner Life of a Cell is badly misleading. It reinforces many educationally toxic misconceptions. Yes, the graphics technology was limiting. But the video doesn't attempt to mitigate the negative impact. For instance, adding a couple of frames of Goodsell's crowded proteins, fading to sparseness, could have reduced its reinforcement of the "big empty cell" misconception.
And it doesn't just hide almost everything (crowded), or slow everything way down (busy), or show completely aphysical rendezvous and docking (random), but it also strings together carefully selected snapshots to tell a misleadingly peaceful narrative (violent).
That kinesin walking along, towing a vesicle? Its "feet" are actually madly flapping around. It is randomly "stepping" back and forth - only its net motion is biased. And between one net step and the next, that big vesicle has been slammed around to every position within reach of that tether. It's a random walk on a leash. Reality isn't a donkey quietly towing a slowly-moving barge. It's a balloon flapping madly in a hurricane, tethered to an intoxicated panicked mouse clinging to a rope.
Biology rides a ragged energetic edge, between things being too strong, too expensive to dis/assemble, and being smashed to pieces too quickly.
More generally, the video illustrates a pervasive problem with science education media. Even when done "well", some aspects are done with great skill and care, while other aspects are silently left utterly bogus. Pity the students, who lack the knowledge to sort out which is which. So rich ecologies of misconceptions are established. And are intractably expensive to displace. It's so easy to create content that leaves students worse off than if they had seen nothing at all. So that's, in general, what we create.
The violence of nanoscale is a critical, defining characteristic. That so many biology undergrads are unclear on it, let alone high-school and primary students, shows just how very far we have to go before teaching deep understanding, transferable knowledge, and cross-cutting principles, finally becomes a reality. Or more upbeat, how breathtakingly awesome science education might eventually become.
(FWIW, the top section of my very crufty http://www.clarifyscience.info/part/Atoms might help some with getting a handle on at least the size aspect of small things.)