I'll try to answer this and anyone is willing to correct me. I do lack some experience at siege, and I clearly admit that, but this is what I think about the 3 classes.
Of course I'd go with the mainstream, ForceMaster. I mean it can kill all class. And thank Macro for that. I haven't tried it yet, but someone told me that a YJ can't kill his FM on its full STA equip. I could be wrong. But basing my conclusion on that said sentence, that's just shows you how well-rounded FMs are with their 2 sets of equips. And I gather that even Arca's EVA can't kill FMs in their STA equips fast.
With Harlequin, sure it can kill FMs at full STR equips. And that's its only chance. Though as the cliche goes, DI is really a beneficial skill. As well as Pandemonium. But with their full STA equips, though it can kill some hybrid FMs and full STR FMs, it just doesn't have the chance to kill FMs at STA equips. Basically, DI is really useful and perhaps their advantage at siege.
I rarely know anything about Arcanist. All I know is that they have to use 2 sets of equips too. Then spam EVA around. I don't know the max hp of them in their STA mode. But I'm sure that FMs can still kill them though I'm skeptical about Harlequins.
So, yeah. I feel like I said something wrong about this but nonetheless, anyone is free to correct me. And perhaps state their own opinion. I apologize for that being much of a help here.