I don't want to just mimic 'depends on the setting', but I prefer to think about it in terms of how advanced becoming transhuman is. Deus Ex is just starting the process, where you can replace parts of yourself with similar or better versions, but Altered Carbon, for example, lets you replace the entire body and upload the mind digitally. Therefore:
For Deus Ex, unless it changed in Mankind Divided, I'd suggest just using Cybernetics as-is, with the option of allowing a character to have their Cybernetics destroyed rather than suffer death or otherwise truly permanent Critical Injuries (IE, at the start of the game, he loses pretty much everything to an explosion and has to have it replaced - just use that system in reverse. Don't want to suffer a 124 Critical roll? Sacrifice your arm (possibly again) in order to avoid the Injury).
In a setting closer to Altered Carbon, where (in the Netflix series) it appears you are simply put into a sleeve based on your existing genetic information, you'd build a standard character, probably have some upgrades that are cheaper cybernetics, with the expectation that you'll 'die' every so often and have to replace it all. Might even allow characters to purchase upgrades to their cybernetics that mimic Talents, since all it takes is one really bad encounter to take it again.