I do agree that Swim Speed can in some ways replace Quick Respawn, but Quick Respawn is still useful in itself.
But looking at abilities head-to-head, while useful in understanding their mechanics, belies that the best strategy is often to synergize rather than stack. If you want to get back to fights quickly, the best way isn't to go 3x Quick Respawn, but 1x Quick Respawn, 1x Quick Superjump, and 1x Swim Speed. Similarly, if you're inefficient in ink, I believe you can get more mileage out of 1x Ink Saver Main, 1x Ink Saver Sub, 1x Ink Saver Recovery than any stacking of one individual skill. If you want to move fast, you need both Run and Swim Speed. And if you're out there trading hits with shooters at higher levels, it's best to bring Damage Up and Defense Up together to have an edge.
Though I stand by my contention that there is no inherent negative correlation between popularity and skill, I'm getting a feeling I may have underestimated the popularity of Team Nice. But I actually always pick what is true for me personally, and this one is as tough as burgers vs. pizza. Leaning naughty.