If we're getting into the nitty-gritty of this, then for me the biggest thing in favour of the loading bay is not the internal storage - it's purely how much it effects the throughput of cargo to the shuttles. The main job of the shuttles is getting things - personnel, engineers, useful equipment, supplies - from Point A to Point B in a way that is not convenient or possible to use a transporter through. This means that the actual logistical chain involved, how long it takes to load a shuttle with what it needs, how many steps that takes, is actually crucial to the ability of the ship to sustain a big operation, to "surge" supplies or people, and so on. One could plausibly imagine a situation where a ship has twice the shuttles but less ability to actually sustain an operation, because the shuttles are all kept waiting whilst guys with handcarts have to schlep stuff up from the cargo pod.
The key question is, should we imagine that Starfleet are this stupid? Or should we imagine that the shuttle bay has at least some ability to pre-cache supply crates next to the shuttles, that there are specially designed turbolifts from the cargo pod to the shuttle bay to expedite the loading process as much as possible, etc.?
This still might not be as useful as having cargo bays right next door, particularly for surging a massive amount of supplies in a very short amount of time depending on how things are configured. But it massively changes the implicit trade-off here, and realistically the only way to clarify is to ask
@Sayle. I am slightly disheartened that rather than asking and risking getting an inconvenient answer, people instead instead kept going with their own interpretations which favoured a particular vote (whether for or against, not singling anyone out here.) But only slightly disheartened, because this happens to some extent with every quest vote where different interpretations of the vote option areuseful weapons in vote arguments.
Anyway, I'm not hugely invested in this vote and actually initially voted for the loading bay before deleting it, I think both are fine and cannot radically mess up the ship. Excited when we get to the internals, and I can annoy half of the thread by aggressively stanning for us to include at least one Science option.