I can't really comment on whether a real amp is better than a simulator since it's a question of personal taste, I will agree that they are two different animals. What you use really depends on what you like versus what's convenient. In the end, both can be made to work for any particular situation.
No matter what the case is, you have to take into account your entire signal chain. With using an amp simulator, I think it's even more important to pay attention to your setup. While you don't necessarily need to spend thousands on a preamp, the pre built into your audio interface may not do your guitar justice. Again, it's a matter of personal taste.
A real amp is always going to have a certain amount of personality and character to it since two of the same model are never exactly the same. An amp sim should always sound the same when you pull up a particular preset. The only thing that will change is what's in the signal chain before it. Your perception of how good it sounds is also very much determined by how your monitoring the end result. It find it a little hard to judge the quality of the sound without a decent pair of monitors.
This is a really good article where Bob Moog explains what he felt was the difference between digital and analog. While it talks more about synths, I think that the concept can still be applied to this situation: http://moogmusic.com/legacy/conversation-bob-moog-analog-vs-digital-sound-generation