These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Anvilicious: Not by as much as the critics made out, but the film does have a much more overtly Christian influence than Bruce Almighty did.
Esoteric Happy Ending: The ending glosses over the millions of dollars of property damage, the hundreds of people who probably died, and the fact that everyone on the ark, such as the Baxters, has lost their homes and possessions.
Which is actually a huge improvement over the original scripted ending, which had no twist to the scenario at all; there's a world-ending flood and the ones on the ark are the only survivors. Naturally, it didn't take long for everyone to figure out this might be a tad depressing for a goofy comedy, never mind that it makes the animals showing up nonsense. And that it would make God an even bigger Jerkass God (If not outright God Is Evil) due to the fact that the original story of Noah's Ark ends with God explicitly promising never to destroy the world via flood again.
And it's all pretty Harsher in Hindsight considering what happened when New Orleans got flooded for real.
God Is Evil vs In Mysterious Ways: On the one hand, God could have had Evan reveal that the dam was flawed and have it fixed or something so that the flood would not have happened. On the other hand, he could have done nothing and everyone would have died in the flood.
The fact that the flood was caused by humans and not by God further complicates the matter - should he have let the humans suffer the full consequences of their own mistakes? Stopped the flood before it began but risk that the ones responsible would not have been hit as hard by the reveal and may have been able to talk their way out of it and go on to do it again?
Special Effects Failure: The flood scene was the main reason why this was the most expensive comedy ever produced (enough that the film had no chance to make back its budget after its tepid opening weekend) and most critics were not kind in saying the flood wasn't exciting or striking to watch, to say the least.