Actually that's 2 different problems
The isometric one is mainly because MOAI doesnt support isometric maps (
see that previous post). Paxton hare made a patch. Now combined with RapaNui, it gives results, but it's not perfect. I'll work more on that.
The second part is coming directly from the
TMX map format page. Tiled, the software i used to generate those maps (which is widely recommended around here) allows different way to
store the map infos (full xml, which you are parsing, csv-based, the one i illustrate
in this post, and base64, which encodes the whole stuff in a base64 hash).
Which means that even for a 2d side scrolling level, you can have a csv or a base64 map. You can use a plain xml file, but, even if it's text, this creates ridiculously long files, which are a pain to read as a human being (for instance, my 10*10 iso map writes 100 lines
per layer because each tiles must be written, even empty ones), and of course, increases the file size (even if it's not an enormous size, it's still bigger in plain xml - for example, my reference map is 11KB in plain xml, and 2KB in csv format. I let you imagine how it scales on bigger maps, for a 2d side scroller, where you can have very long levels

).