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As for Slug B, that will usually be the one that pops up first.
I might give it some though to switch when I get specific augments. Those being the medbots, DNA bank and Recon TP. But even then, I'll generally stick with what I got.
Both have their positives in negatives, and it's fairly easy to work with them.
They are used differently in different situations. For instance, getting boarded means either fleeing to medbay whilst clonebay allows you to completely vent the ship or suicide your crew on them.
When playing vanilla, it seems clonebay has more going for it though. As far as blue options go and of course being able to put the life of your crew on the line in some events. Naturally, you have to take crew experience into account, especially when using a boarding strategy.
On a regular gun-ship, it doesn't matter nearly as much and you're definitely best off saving your money and sticking with what you have. Medbay is nice for keeping your crew topped off anytime there's downtime in a battle, but the clone bay is nice for preventing Unfortunate Accidents. They both have their own niches.
I guess one thing that does annoy me is that a few ships have a clone bay located in a 2x1 room, with the cloning apparatus taking up one tile, so that means only one person can repair it at a time, which can be aggravating. On the other hand it can do funny things to the enemy boarder AI when one of them tries to go to the clonebay and the other tries going somewhere else, so it's not a huge loss.
Each has its advantages. For instance, medbay is definitely better as a defensive system.
Otherwise I'll takes what goes with the ship.
Why does everyone rant so much about "Backup DNA Bank?" That augment has never been neccesary - my clone bay has stayed online just fine.
The augment isn't usually worth the slot to me, so only to be kept if there are any free ones left.
Remembering what you have is definitely very important, though, the strategies differ so much you can mess up your boarding party if you use them wrong.
of course, if im doing boarding and get my hands on a reconstructive teleport, then i try to get a clone bay, because that combo is powerful indeed.