I just wrote this in the dream thread:
After waking up from that dream I couldn't shake off the feeling that this was worth poking into, although the theory as it stands in the dream has some serious flaws (ignoring the 6 (?) year gap, assuming the poisoning happened at the Terry Fawles trial and that it really was his mug itself, which he offered to Terry, that was poisoned, etc.) so I went and made myself a cup of coffee and tried making something at least plausible of it.
This is all just for fun.
The core of it: Diego and Godot are not the same.
I've come up with two different explanations for the story behind it: the first one is that Godot was asked and/or hired by Diego himself to "return" while Diego went somewhere else to start a new life. The reason for this could be two; either Diego wanted Godot to watch over Mia (if he didn't know she was dead) and/or Maya and possibly the rest of the Fey clan and make sure they were safe and all. Or it could be that he saught for revenge, although he didn't plan on having anyone killed, that was just Godot getting caught up with it all and refusing to pull his ass out of the fire.
The other explanation is that Godot is an imposter who stole Diego's identity for whatever reason. Diego himself is still in a coma, or he has died.
Also note that it was stated in the game that Godot is really good at imitating other people.
What is questionable in this theory is a) the 6 year gap and b) the Godot persona, because it's both a shitty disguise and a shitty impersonation of Diego.
A) The explanation for the time gap is simple. As for the first theory, that was the time it took before Diego woke up from his coma. As for the other, Godot stumbled upon Diego after the latter had already spent years in a coma, or that was the time when he died/ was plugged out (by Godot?)
B) As for the first theory, this was excactly the point. Godot wasn't meant as a perfect impersonation of Diego, but rather as an observer, working from behind the scenes and keeping an eye out, a guardian angel, if you will (alternatively a death angel for the vengeance theory). Godot isn't a name, it's a code (as we've seen how it ties into the name Diego Armando), and that along with the similar but not identical hair and clothing serves to see if anyone will recognize him, if there are still people out there thinking of him. And as for the second, Godot couldn't legally take Diego's name because Diego was legally dead, and it would mean a risk of being discovered by some authority. The white hair and the visor? That was what Diego looked like while in a coma, when Godot saw him. Godot could be his twin, regular brother, some other relative or a doctor or even another patient who randomly happened to have a similar downer half of the face. Or... to drive this even further into the crazy territory; Godot is not wearing one mask but two, and he's really a spy who's special ability is to mimic people perfectly. Nudge, nudge.