Until earlier this year my answer would have been "What tilemap system?", but now that Unity also has a tilemap system, and even extended it with support for isometric maps just 3 days ago in Unity 2018.3, it is an interesting question. If you're using Unity anyway, then I would suggest trying out both Tiled (possibly together with SuperTiled2Unity) and the Unity tilemap tools to see if you can find an answer.
In general, there are several basic advantages to using Tiled:
- Tiled is free software. This means anybody is free to change it and to redistribute changed versions. The tool is effectively yours, while Unity is theirs. There are also no restrictions on what you can do with Tiled, or how much you can earn before it stops being free.
- If you use Tiled, the maps you develop for your game are not locked into Unity. They are stored in the open TMX map format or as JSON, with support libraries available for most programming languages. You can develop your game using any language or framework and publish to any platform you like.
- Tiled runs on GNU/Linux, in addition to Windows and macOS.
There are many features in Tiled that are missing in Unity's tilemap support, but obviously Unity will have some features that Tiled doesn't currently support as well (like scripted brushes, but they will come to Tiled soon). Both projects are actively maintained and continue to be improved.