There's also the notion that some characters are a 'good fit' for an assist trophy and might stay there permanently, like Lynn. Maybe it's because they're not really relevant to a large amount of people or maybe it's because they are characters that aren't really able to be fleshed out into a fully playable fighter. Not saying isaac or ray deserve to permanently be assist trophies, because they have enough versatility to be full playable characters, but it's also possible sakurai and team think they're a 'better fit' as an assist trophy than as playable.
I'm all for isaac being playable, I think he'd have a cool moveset, using the djinn's powers and all. Same w/ ray having tons of cool custom robo abilities. But where they fit in my mind (this is just me personally, not you, or sakurai!), they're not really 'visible' enough to be smash bros fighters, so I'm just not getting my hopes up. I think an addition has to make sense. It has to be able to get more "Wow, that's so cool that they added so and so" responses than "who on earth is that?" responses from the public at large.
And if they do get the 'who on earth is that?" response, they need to be quirky enough that it's quickly forgiven. Isaac and Ray just look like generic video game characters in the grand scheme of things.
One again, not trying to upset any isaac or ray fans, I'm just saying how I see it. If I were making smash bros, I'd keep them at assist trophy level. Fortunately for you guys, I'm not!