My changes would include:
1 - Making Cross Class Skills a point-buy system rather than fixed slots.
Some skills would "occupy" 6 points, others 3, etc. We might then have real options.
2 - Adding some more procs/effects that make our rotation more dynamic - providing opportunities for great players to rise above average players through skill/decision-making.
3 - Make Materia more reminiscent of FF7, in particular Blue Materia.
Here's the thread where I added to liljramos88's suggestion:
http://forum.square-enix.com/ffxiv/t...ria-system-Pls

Here is also a doc I made while providing feedback during closed beta:
https://docs.google.com/document/d/1...EA4BgviOsI/pub