Christianity is indeed full of problems, loopholes, and moral issues. Anyone who reads the Bible will quickly discern all the ethical, moral, and intellectual problems that it contains, which are all problems in and of themselves. That said, the biggest problem with Christianity is the concept of eternity and who spends eternity where.
Let's back up for a minute and see who all is in hell. Let's take a few names of some non-Christian people who influenced society for the better: Gandhi (Hindu), Abraham Lincoln (Deist), Confucius (made sort of his own religion), Susan B. Anthony (atheist), Andrew Carnegie (atheist), Elizabeth Cady-Stanton (atheist). None of the above were Christians, yet they did great things for society. Guess where they are? You guessed it, they're burning in hell.
Now let's see who all's in heaven, shall we? Names like Adolf Hitler (Roman Catholic), Timothy McVeigh (a professing Christian), Jeffrey Dahmer (a fundamentalist Christian), David Berkowitz (a professing born-again Christian), Bruce Lee (another professing Christian). What do all of these names have in common? Of course, they are all serial killers. However, they were all Christians, and Christians go to heaven because Jesus supposedly atones for all sins, no matter how great.
So now we see the really big problem here. All of these evil men are in heaven because they happened to believe in Jesus as the savior and messiah and got off scot-free despite their evil deeds. The people in the former group were truly wonderful people, humanitarians who contributed to and advanced society. Despite their good works, because they didn't happen to believe that Jesus was it, they're all burning in hell.
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In reality, each group deserves each others' fate. The former group doesn't deserve to be punished in hell, they deserve to be in heaven. Serial killers deserve to be punished in hell. That, my friends, is the biggest problem with Christianity.