I do know that all LIs are toxic to some extent with MC since they are monsters after all.
HOWEVER Simon seems much less toxic to me than Isaac. Because if you exclude the experiment mini-event, of course, we do have some free will and freedom of choice in his route, compared to Isaac where you're held captive in the castle against your wishes and treated badly every time you express your wish to leave or to be treated like a human being. Simon is also much more nicer to MC and not prone to unpredictable mood swings.
I do agree that drugging and experimenting on MC without prior consent makes him a dangerous and untrustworthy person and I don't condone what he did at all, just to be clear. I even picked all the power oriented choices because the whole ordeal made me feel uneasy and upset. However I do understand his motivations for treating MC like so, unlike Isaac who's just...toxic for the sake of it, without a real purpose for it. (Also, experimenting on carriers would be pointless since they do not carry the Resilere Allele, the gene the Institute's been trying to replicate for centuries.)
Hence why I was surprised to see Simon ranked last in your post. I wasnt trying to convince you nor implying that you were wrong since this is not "you're right/wrong" situation. I don't dislike Isaac either, let's just say that I'm not as emotionally invested in his route as I am with Simon.
I'm also a fan of body horror and a science nerd who works in the medical field so picking Simon over Isaac is a given. xD