The doubts I have about any all-powerful 'higher power' stem from the fact that Crayak was very quick to copy the Ellimist when he ascended. As the Ellimist points out, the odds of what happened to him were very small, but the odds of it happening again (IE, after Crayak realized what the Ellimist had done) were great. If Crayak was such a quick learner, and he had lived in the shadow of an all-powerful higher power for most of his life, wouldn't he have figured out their trick, as well, and thus become all-powerful himself?
That's assuming that whatever higher power casted Crayak out had gotten powerful with a gimmick (like the random event that happened to the Ellimist) that could be recreated (as Crayak did with the Ellimist). it could easily be the case that the higher power was created as a higher power; it simply was, and there were no steps to become what it was.
Sports analogy, but as much as I copy the running style of a certain player, do the same training regimen and so on, I can't gurantee that I will 100% match him or replicate him. For humans, the limit is genetics; no amount of hard work on an average person will exceed the same amount of hard work on a person with good genes.
Likewise for Crayak, the Higher Power could be on a level that could not be replicated or matched. If we want to compare the higher power to god, and crayak as an angel (I don't subscribe to this, but it's just an example) how would an angel ever match God himself? If he could, the angel might as well be God.
And besides that, as others have already pointed out, wouldn't a truly omnipotent entity have been able to stop Crayak from becoming as powerful as he currently is? And wouldn't an entity at least benevolent enough to have seen Crayak for the evil and dangerous being that he is, have been compelled to do so?
Except we don't know whether the higher power was omnipotent or not. If he was truly omnipotent, then of course he could easily destroy Crayak, fix the wrongs of the entire series, make it so that the entire series and the universe within it was a god and happy place; but if that was the case there would be no story. Furthermore, it would made this 'Higher POwer' essentially a 'super ellimist'; a cosmic do-gooder.
Perhaps the cosmic higher power threw Crayak out because simply put, that higher power had chosen the role that the Ellimist initially offered to Crayak after they ascended their physical forms; the higher power chose to be the role of an observer, allowing things in its universe to go without interference; Crayak meanwhile would never have subjected itself to merely watching, so instead of proposing a game to play (as the Ellimist did) the higher power casted him out, simply because it was strong enough to do so.
The ellimist, meanwhile was not strong enough to do the same, and Crayak was stronger than before, so they chose to play a game.
As for why the ellimist never bothered to destroy Crayak when he had the chance, it was probably because he now had seen the future; Crayak and Ellimist had their parts to play. If Crayak had been destroyed, books 48, 27, 26, 7, 13 and any book that ever featured the Ellimist or Crayak would not have made sense since some of the actions done by the characters were a result of the games between Ellimist and Crayak, and some of the actions the Ellimist was forced to make (for example, never directly assisting the animorphs) would have been irrelevant seeing as those were 'rules' that only existed when he played with Crayak.
If the ellimist had his way, the war between the yeerks and the andalites need never have happened. The animorphs would never have needed to fight, and all in all, the series would have been vastly changed. Knowing all this when he ascended the higher plane, the ellimist could have chosen not to kill Crayak when he had the chance; in continuity; because he knew the roles that he and crayak would have to play.
Undoubtedly though, this means that everything that animorphs had done was predestined to happen; none of it was accidental; their meeting with elfangor, aximili, and so on.
I personally don't believe the Ellimist would ever be lonely; he had found joy in playing and living life, for him and he was filled with the essences of hispast, present and future. He could create anyone he wanted to talk to, inhabit any being or create a being to live amongst species.