They have more cavities in their hull and respond in much more... interesting ways to outside pressure than a smaller, more compact sub. Sure, there are upsides; storage, more hull points, harder to munch on, et-cetera... but overall, it'd be much better for exploration's sake to have a smaller, more-durable sub than another large one. (I speak, of course, of the upcoming DLC). Not that I have anything against the larger vehicles which are rumored not at all- it's simply a fact that another cyclops isn't ideal for exploration or deap-sea diving.
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