This is one of the questions that programmers are coming up against when designing an RPG or Adventure type game. Mainly, it comes down to preference. Some programmers may choose a square tile base look because the algorithms for drawing such tiles is much easier to figure out but, even then, they come up with a few problems. By saying 'square tile base look' I mean with only the north walls showing. Here, I will discuss those problems and their solutions using an isometric style.
The main problem, with a square tile based look, is how to show the flat sides of objects and walls. It is easier explained in figures 1 through 3.

According to Figure 1, there is an opening beside tile #2, which is labeled as tile #3. Showing north walls, In Figure 2, tile #3 isn't visible. In many RPG games that I have played, using the style of Figure 2, either a character standing on tile #2 couldn't go down any further, could go down but be hidden, or the tiles X would be shown. Because you can't see an array map such as Figure 1, in most games, you may never know if the two X tiles existed. Because the walls are 2 tiles high, it would make sense that a wall below the bottom X tile would cover both X tiles. Also, in most cases of Figure 2, it may be hard for players to determine where the opening, beside tile #2, is because it appears above tile #1.
In Figure 3, you can see tile #3, and it is easy to tell that you have to be standing on tile #2 to get there. The X tiles are also very visible here. Even if there was a wall below the X tiles, you could still see that it was there. You would not be able to see if there was an object on tile #3 in Figure 2 but you may see it in Figure 3. Either way, it is a good idea to hide walls that are obstructing the players view.
So, there are many advantages to using an isometric style as opposed to a square tile based look. You are not forced to show only north facing walls. You can feel a lot better making west and east passages. I've also noticed that, in those cases, there is a boarder above all walls in square based looks, which doesn't look good and isn't needed in an isometric style.
The only disadvantage that I can see with designing an Isometric style
game is that you may find it harder to draw objects from an angled view.