The Train is just an in-battle animation, not something story based. I don't count Sephiroth destroying the universe multiple times either.

Ghestal Knew Kefka was pure evil, that's why he used him. Kefka was willing to do the diabolical and horrible trout the emperor needed done. Kefka usurping him was more Ghestal thinking he could control Kefka, not so much that he trusted him.

And the Opera Scene? Really? Celes looked like Maria, this happens in real like. I can recount at least three times I've scene a guy who looks practically Identical to someone I knew, enough so I started talking to them like they were that person. Celes looking enough like Maria to be mistaken for her is no way a suspension of Disbelief.

And yeah, games have trout that are 'unbelievable'. This is not the same thing as breaking the suspension of disbelief. That very term means your ability to suspend your belief of what's possible. For example, magic is not possible. However, for purpose of a story, I'll accept it's possible in the world.

Clouds Sword would be unwieldy as all smurf, yet I can suspend my disbelief enough to run with cloud wielding it effectively. Especially since they at least give him the reason of being enhanced by Mako, giving him more strength then a normal person would be capable of. This is a game where only people who have this super human ability seem able to wield more absurd weapons.

The Gunblade is a large sword with a pistol grip duct taped onto it. Why is this harder to establish my disbelief for? Well for one, I cannot fathom an advantage to holding the weapon that way. And the way it works, using the force of the bullets and what not to create a vibration in the blade, would not require you to hold a weapon in a way that would smurf up your wrist by giving it a good swing. Mind you, the suspension of disbelief may vary from person to person. Glad I could clear up the misconception for you.

Though if you'd like, I could give you more ways the writing itself is bungled up in VIII!

(SPOILER)Seed shows up on T.V. when attacking the president guy, and everyone looks at Zell like he's a smurfing Idiot for announcing Seeds involvment. No one looks at Squall and Seifer as if they are idiots, even though they are wielding gunblades. These are weapons the game established early on are ONLY used by members of the Garden.