I've heard this line of reasoning before, not in reference to Bioshock but other games, and it's redonkulous. Unless you can upgrade them all RIGHT AWAY, the ability to eventually upgrade them all does not negate the choices of what to upgrade first.
If that was the only problem surrounding the significance of chocie in the game then I woudl agree with what you are saying. The problem is that NONE of the small choices that are in the game really matter, so you get a lot of little issues adding up to one big issue. Even your plasmids and tonics are infinitely swappable. I don't have to make any decisions that I have to live with for the rest of the game. Even rescuing the little sisters instead of harvesting them doesn't really "hurt" your adam collection since you get the little present from Tenebaum for every three sisters you rescue, which is way more than enough ADAM to do whatever you want.
Isn't that true of all FPS games? Crysis, which you go on to praise, doesn't even have a pretense of temporary choices. You can choose to make your suit this or that, but then switch right back on the fly. You can choose how to set up your gun then switch it right back on the fly. What decisions do you have to make in that game that you live with for the rest of the game? At least in Bioshock you have to live with your choices right now, unlike Crysis where you live with your choices never.