I think it's really not bad though I admit I'm pretty unusual in liking most of the kind of comedy it had. But while a lot of people really dislike that kind of comedy if it didn't have it I don't think they would like the film much more, if it didn't have it it would instead just feel pretty basic, still otherwise undeveloped.
Re: with the religious subject matter, the Indiana Jones movies were able to involve religious artifacts having magical powers without being particularly controversial, though they of course only focused on the artifacts' power and implicitly nature in the endings, the rest of the movies just focusing on the character interactions and actions (and some humor). And in TFF Sybok's motivation is also pretty not focused on and/or not stated until the end. Maybe it could have been better if he had openly early stated he was trying to find, go to Paradise but still not focusing on it, what that meant, what it related to until near the end.