A few similar topics to this already, but you could play Zeta/Omicron or Rejuventation. Uranium has some potential but it uses a pretty buggy Essentials, the story is slow, and if youre not into tons of Fakemon you will be upset. Pokemon Island is good if you dont mind a nonexistant story and bad graphics but its redeemable in being purely about battling which makes it a niche game. Gray Topaz also has some potential but personally I couldnt get over the character sprites and quit the game before I even got a starter but may be worth checking out despite my personal bias.
Theres a lot of other games that seem good but Im waiting for them to show signs of developed progress.
For a bit of a twist there is Digimon Digital Dream which while not strictly a pokemon game it is built with essentials and incorporates pokemon mechanics. Its downside is it also uses a buggy version of Essentials.
just noticed this one:
http://www.pokecommunity.com/showthread.php?t=286748
Looks fairly impressive, Im actually gunna download and check it out myself right now.
Hmm nevermind :/ it actually only has two gyms so far and the developer doesnt want to release an update till its *perfect* and prob wont be done till like december. Ugh, I much prefer rolling releases.