Anyways, I have some suggestions.
Base the Starters around the desert.
Pokemon such as Cacnea and Trapinch make sense to me. You stated in the OP that it's a desert-like region, why not make sense flavour-wise?
Develop the story-line more.
I love that you have an original region and team, so you should develop a better storyline around them rather than they want to "control the region by capturing every Pokemon." Great hacks have always had great storylines behind them.
Make your Legend Fakemon theme-based.
In relevance to the poll you have up, I'm really hoping the Fakemon legend is very Desert-based and could know Sand Stream as an ability, tying in with Kyogre/Groudon/Rayquaza, as I'm sure they'll be included in the hack.
Just some stuff I came up with, not saying you have to use it but it's all ideas I feel could make the hack way better.
Oh, wow, that's great! I didn't except for that massive help :D
Can I contact you with other way instead of PMs? :D