As someone who wrote one of those 2D-ish isometric games in the 90s, it was hell. All the problems with trying to render the tiles properly and figure out what tile the user was clicking on when some tiles are semi-transparent etc. The artists need medals though for creating amazing levels with tiny palettes of pieces to work from.

We made it especially hard on ourselves by having 3D characters interact with the 2D tiles:

https://www.youtube.com/watch?v=9UOYps_3eM0

I absolutely adore the look of isometric, though.