If you think KH's plot hasn't become convoluted, we are just going to have to agree to disagree on what makes a coherent and enjoyable storyline. I love Kingdom Hearts to death, but that plot is an abomination. It's poorly paced, retconned to death, and full of meaningless and unnecessary convolutions that the scenario writers at Square seem to think are making the story more ENGAGING. They're not, they're turning it into unrelateable pulp anime schlock. The unneeded story added by the side games was fine when it was just Birth by Sleep and 358, but all that extra "stuff" has irrevocably changed the stakes and the scale of what is happening.
BbS had the story going in a fantastic direction, and then 3DS comes along and (spoilers)
Adds dream worlds, time travel, revives every character ever killed in KH2/CoM, and then still manages to not resolve anything. Oh, and let's not forget that out of nowhere, the Xblade is suddenly incredibly important and Xehanort's master plan is to clone himself several times, across time, which he somehow knew he'd need to do before he even could have known, in order to wield this blade, to bring about a Keyblade War for Reasons (TM). Oh, and all of the OXIII members are okay with being cloned on top of.
Yeah, no. KH's plot is a convoluted mess.
And let's not forget how horribly they've marginalized Donald and Goofy, which is the most unforgivable crime of all.