I gotta offer my perspective as an Arthur-did-it truther :p
If we focus only on what we know pre-decision, we have the knife and the book that speak against Arthur already, and also a very angry diary entry by him that basically calls Theodore stupid for only caring about the elephant and not for their project:
"I must think, lest out invaluable history be buried by the inconsequential." -> this quote alone suggests he wasn't going to sit around and let Theodore ruin the site and turn it into baths. He was trying to come up with a plan.
Shortly after, their partnership ended. Arthur's motive was never that he couldn't co-exist with the elephant, but that Theodore, who was the sole proprietor, didn't share his vision on the future of the site. He didn't share the passion and cared about his elephant more, and his carelessness destroyed their partnership.
Arthur, on the other hand, saw the site as his most important achievement in life and he is said to "have sacrificed almost everything to get it".
His interest is described as obsession. Yet, he was about to lose funding because the whole project was funded by Theodore with whom he quarreled, and that after he's already used up all his resources on the site.
Why wouldn't Arthur, whose dream was about to be destroyed by Theodore, use that very elephant to destroy Theodore, in return? After months and months of resentment and trying to find a way to save the future of the site?
Arthur is a man portrayed as desperate and paranoid enough that, even though you find the tomb, he becomes hostile towards you and accuses you of trying to steal "his" discovery.
We also know Arthur was supposedly injured while digging, but we never actually see him do any manual labour while we are there and looking for his tomb. He doesn't leave his tent at all. And yes, the workers have the same vest, but FW also reuses assets a lot and I don't see that as evidence that the slot was supposed to stay empty and that there was no knife.
Arthur supposedly only owns the book to educate himself about the elephant, but the article itself notes that it contains a chapter about the danger coming from elephants in heat.
I don't believe Arthur when he says he wanted to learn how to understand the animal. I don't see why I have to believe in anything a possible culprit says unless there is evidence. And the man had devoted his life to his digsite to a point he neglected his appearance because of it, as stated above. I would say he did not have the time to educate himself about the habits of an animal he didn't care about and begrudged Theodore for having.
Paul, on the other hand, has no real motive to attack Theodore after he's already packed his bags to disappear with Imogen and escape - they are about to leave Cordona and won't be bothered by him at all anymore. Theodore might have been a threat to Paul in the past, but not in the future.
Moreover, we don't know if they were planning to leave immediately. We don't know if Paul really wanted/needed to distract Theodore to get Imogen out - she could have simply left the manor while her father was sleeping instead of taking the risk of being caught by having Paul distract him while she was carrying multiple suitcases.
And in general, Paul's alibis is more believable. He was beaten up - we saw the threats. He says he was at the hospital - he don't visit it in the game, but if we apply real world logic, we could actually ask in the hospital if he went there.
But nothing Arthur uses as an alibi can be confirmed. To assume he is innocent, we have to take everything he says by the word - that he never had a knife, that he injured himself while digging (which we never see him do), that he was merely interested in the elephant. He can't prove anything he claims.
Also, about the stones that Imogen threw - when you consider where they landed, you can assume that the elephant was right in front of the gate already by the time she got outside and started throwing. The elephant would have covered the gate and she wouldn't have seen who was hiding behind it. The culprit is only visible in the imagination sequence because the elephant is still a few steps before the gate, but this is not where the stones landed.
This is what I mean, if Jon was Imogen and threw a stone in that direction, then her target is likely right in front of the gate, and her target was large enough:
And to come back to the decision:
Arthur never says he didn't kill Theodore if you tell him you'll let him go. He says Sherlock came to his senses right after Sherlock accused him of murder. That, in itself, doesn't speak of an innocent man to me.
And last but not least, Arthur is not an elderly man, either. He might not be as strong as Paul, but he is apparently strong enough to work as the site to a point of injury. Unless he lied.
Anyway, I wanted to offer my two cents because I saw your comment saying how the game should present the facts before the final decision is made (as a reply to me talking about Arthur's reaction to being accused but let go), and I felt the need to show that the game does present a lot of facts that point towards Arthur :D People don't believe that Arthur did it just because of the reward, but because many believe he has the strongest motive.