Problem was that the original scanner was twitch-based, which fit as well as the original casino interface fit Engineering.I think the idea of the 3 samples came up when they had to get rid of the first incarnation of the Bio scanner. Maybe they thought they had to find some kind of compensation for the lost tormentor. This is what happens when you take minimalist game design to the extreme.
the edit below came shortly after the +1 (sorry @Linnunrata, just take it back if you don't agree)
But what a missed opportunity to kill several birds with one stone: a bio-scanner mechanism that makes it dependent on the personal skill whether and how much of the remaining two samples still have to be scanned. I could even imagine a kind of hybrid between the original scanner and the current situation...
Leave the multiple samples needed, but vary the amount based on skill. Make skill a puzzle-related one (match up DNA patterns or cluster patterns or whatever). Vary the difference between sub samples taken depend on physical distance between sample locations, so there will be a tactical element as well (further travel = larger chance of a useful sample).
And so on.
Unfortunately FD just have a pile of cards with a variety of phone-app gameplay loops on. These are stored in a big floppy hat, which is consulted when something new is added to the game.