I think the main objection to Ark Encounter is the millions in state tax subsidies and the religious hiring discrimination, not the theme itself.
The "God Theory" is not, strictly speaking, a theory, nor is it within the purview of science. Science can only deal with tangible evidence; with things that can be seen and measured; with ideas that can be falsified. The supernatural provides science with nothing to work with.
Why can't a creator be a theory? You're just presenting a strawman saying it's not science. The idea of falsification is being challenged because it eliminates ideas such as the multiverse, something from nothing and other theories from being discussed. Even Karl Popper started to question it.
GK Chesterton (who first proposed falsifiability), a creationist and author, said it best,
"Science is weak about these prehistoric things in a way that has hardly been noticed. The science whose modern marvels we all admire succeeds by incessantly adding to its data. In all practical inventions, in most natural discoveries, it can always increase evidence by experiment. But it cannot experiment in making men; or even in watching to see what the first men make. An inventor can advance step by step in the construction of an aeroplane, even if he is only experimenting with sticks and scraps of metal in his own back-yard. But he cannot watch the Missing Link evolving in his own back-yard. If he has made a mistake in his calculations, the aeroplane will correct it by crashing to the ground. But if he has made a mistake about the arboreal habitat of his ancestor, he cannot see his arboreal ancestor falling off the tree. He cannot keep a cave-man like a cat in the back-yard and watch him to see whether he does really practice cannibalism or carry off his mate on the principles of marriage by capture. He cannot keep a tribe of primitive men like a pack of hounds and notice how far they are influenced by the herd instinct. If he sees a particular bird behave in a particular way, he can get other birds and see if they behave in that way; but if he finds a skull, or the scrap of a skull, in the hollow of a hill, he cannot multiply it into a vision of the valley of dry bones. In dealing with a past that has almost entirely perished, he can only go by evidence and not by experiment. And there is hardly enough evidence to be even evidential. Thus while most science moves in a sort of curve, being constantly corrected by new evidence, this science flies off into space in a straight line uncorrected by anything. But the habit of forming conclusions, as they can really be formed in more fruitful fields, is so fixed in the scientific mind that it cannot resist talking like this. It talks about the idea suggested by one scrap of bone as if it were something like the aeroplane which is constructed at last out of whole scrapheaps of scraps of metal. The trouble with the professor of the prehistoric is that he cannot scrap his scrap. The marvellous and triumphant aeroplane is made out of a hundred mistakes. The student of origins can only make one mistake and stick to it." G.K. Chesterton,
Everlasting Man, II