Hohenheim is one of the odder characters in FMA 03. It is perhaps one of the clearest symptoms of how the series overtook the manga as Hohenheim’s story in that isn’t covered until much later. Therefore he’s set up to be important but he’s also not meant to be much more than a minor character.
In the manga, I believe Father’s existence was beginning to be revealed (I haven’t actually read much of it, I confess) and it’s not clear at first that he is a distinct character from Hohenheim- the reader is supposed to think it’s Ed and Al’s father. (He looks just like him, you’re not going to assume its his identical twin.) So, it seems Hohenheim is supposed to be both Ed and Al’s father who their mother clearly loved and also a monstrous person who controls the Homunculi and has some sort of evil plot that involves wars and conflict.
03 Hohenheim is an interesting attempt at this I think, as he has clearly done terrible things in the past but he’s not actually the antagonist. Everything we see of him shows someone who’s trying to be a better person or at least move on from his dark past. He doesn’t make any excuses or apologies for his past (avoids talking about it entirely actually) and doesn’t expect anything from Ed or Al either.
Towards the end, Ed does believe it might be his father behind the Homunculi, until he actually meets Dante at the end. I kinda wish this had been emphasised a little more. The ending is a little rushed sadly.
Hohenheim doesn’t actually do much in the series. He confronts Dante, trying to get her to listen to reason and offers Ed some answers and support in the other world. That’s basically it. His past is incredibly interesting though and works as something of a potential dark path for Ed if he had allowed himself to forget his morals and didn’t have his brother’s influence.
(I intended this to be a quick post but now I’ve mentioned Ed…)
Hohenheim created a Philosopher’s stone, sacrificing other lives to do it just as Ed was tempted to do in Lab 5. He also created a Homunculus, just as Ed and Al did, a failed human transmutation that went badly. In fact, Ed and Al learn how to make one by following his notes. Where Ed eventually has the courage to face his creation and fix his mistakes, Hohenheim has been running from his mistakes for a long time. He never even meets Envy (except in CoS). In the series proper, we finally see him facing Dante but it’s far too little too late.
This change of heart probably comes from falling in love with Trisha. Of course, even with Trisha he’s too afraid to reveal his secrets and chooses to leave rather than reveal the way his current body is beginning to rot. Ed has also had a tendency to run from his mistakes and hide what troubles him. The prime example would be how he wanted to ask Al for years if Al blamed him for the human transmutation and doesn’t find the courage until episode 24, after their fight and with some support and encouragement from Winry. But Ed does get better at opening up and facing his problems. When Al tells Hohenheim how he lost his body, Hohenheim’s talks of taking someone else’s body. Al hates this idea though – he and Ed just want to regain what they’ve lost.
In the last episode, Ed seems to hold no anger towards his father, nor does he try to avoid him but he actually opens up to him about some of his worries and it’s a mark of how much he’s grown. For all that it’s said that FMA 03 is a kind of dark story, Ed avoided the dark path. Hohenheim was able to change too even after everything he’d done in his past (his change came as a result of meeting Trisha and falling in love).
I feel like every character, villain or otherwise, is given a chance to change and do the right thing in FMA. (What is right is subjective but they can at least turn away from their past evil acts.) No matter how awful their crimes are. Not everyone takes this chance but it’s there.
Zetalial 