Yeah, I definitely have to agree with you @Riviute that Alatreon is a really tough, but also awesome boss in the MH series ^-^
But as for my entry... idk if it really counts but whatever, it's the End Chapter of Fire Emblem Conquest in Lunatic mode, since it's extremely difficult to do that without losing any units, which even tho it's the End Chapter, as a FE player you instictively don't wanna lose any units if you can help it xD but yeah, First of all there's the Boss, which is a possessed version of the character Takumi, which is able to shoot all your units from a big distance as long as no object is in the way, so you'll contently have to make sure you keep those defensive walls up, which will waste a turn of one of your Royal unit's turn, which generally are some of your strongest units, on top of the Enemies being really tough and more reinforcements will keep coming regularly all over the map until you can make you way to Takumi, and even then he has a lot of health, defence and Attack, and a Bow which has a Range of 1-4 (which is a lot, usualy bows have a range of 2 and are useless in close range aka 1). And oh yeah, let's not forget the fact that he is Paired up with a copy of Himself, lmao. So you'll have to be careful to not make your units commit suicide when you reach him. Not to mention that in general resources and opportunities to grind in the Conquest route is hard except if you buy the EXP/Weapons/Money DLC quest so yeah...
All in all it's a pretty tough fight imo. But also really fun cuz it tests your abilities in how you deal with it.