Namco is very good at changing stories from the game's endings to suit their newest Tekken installment. Take Kazuya, for example: Didn't he die twice? And Bruce? And Beak? And.. the list goes on.

So, if Namco wants Bryan in Tekken 6, then he will be there. Not matter what his ending in Tekken 5 was. They simply say that: A) Yoshi spared his life, or Bryan was not mortally wounded and got away.

Anyway, to come back at the threat's main topic:

Yoshimitsu's armor isn't the same from T4. Maybe the stealth feature meant the armor had to sacrefice it's bullitproof layers. Or maybe Bryan hit him on an unprotected area of Yo's body (neck, legs, arm?)
And well,...I have NO idea why he doesn't have a sword while jumping. Probably a screw-up.