I tend to divide Elias into his different "versions", which makes the question of how I feel about him (them?) a little easier.
Basically, I feel for the teenager, he's been through a lot, first with his mother seemingly abandoning him, then growing up in the system, then going to the Morleys and having everyone basically telling him he is Jesus, but also that he'll kill almost a million people. Imagine having every adult in your life suddenly telling you, yes, you'll find love and people who care about you, but only if you do this horrible thing. It's manipulation from start to finish, and every single member of the cult who ever pushed Elias or Said has a responsibility in this. I know they were all brainwashed themselves, but still. The only one we ever see questioning it is Andrew, and even he does very little.
As for the adult versions, the Commander falls in line with an authoritarian state and pushes its agenda, because he has been told he will get his reward in the end. Manipulates everyone, specifically Iris, shoots Shahara, forces Defoe to assist him. This version of the character is very little developed, but what we have is an opportunist manipulator and demagogue. The most emotional we see him when he yells at Shahara, wanting to push responsibility for their situation onto her.
Then the Harker version, this one is mischievous and playful, and completely callous. Someone here on tumblr wrote about him wondering if he even sees the Victorians as people, or if the whole situation is sort of unreal to him - merely background in the setting of his "just reward". The way he treats Hillinghead is utterly horrible, as is the way he manipulates Polly. I have to admit, I kind of hate him the most, because Alfred is my favourite, and he murders him, twice. I was thrilled that Alfred managed to turn the tables on him in their second prison wagon conversation, and the fact that he needed 50 more years to admit that Alfred was right really drives home how small and pathetic a person he is at this point.
Finally, the old one - I actually have to say fairly little about him? He's a coward, and yes, he comes through in the end, but it still takes Polly killing Esther and then Charles with his smoking gun to show up for him to finally *do it.* I just find it very difficult to feel much for him, no matter how much regret he shows.