You can play PTD3 at http://samdangames.blogspot.ca/p/play-ptd3.htm
Samuel Otero of sndgames, the one who worked on PTD1 and PTD2, stated in his twitter about him working on a new PTD game, Pokemon Tower Defense 3. https://twitter.com/sam_snd_games/status/689627717654941698
The first tweet shown above in the link is him saying that he is making the first scene of PTD3. He said the first tweet in January 19, 2016.Pokemon Tower Defense 3 Legacy is the sequel to both the first two games. The main character is Noah Ketchum who is the son of Ash Ketchum. You will be playing as him when he is young and you will see him develop. In the future Noah will be the leader of Neo Team Rocket.
PTD3 Related Tweets
Alpha 0.1 - First Cutscene, First Level playthrough with Noah and Pichu.
May 4th : Alpha 0.1 - Added Loading Screen. At the start of it you see Noah Ketchum and his partner Pichu, evolving into a teenager at 50% with Pikachu, and at the end is the Noah Ketchum with Raichu, and the timeline when he made Neo Team Rocket.
May 6th : Alpha 0.1 - Added Level 2, Diglett's Cave, Added Cutscene 2.
June 11 : Alpha 0.2 - Added Saving Feature & Elemental Pokemon. You can login with your PTD1/PTD2 account.
June 24 : Alpha 0.3 - Released a small update for PTD3, it includes the pokemon info screen, ability and moves changes are now saved, and you can release pokemon
July 16 : Alpha 0.4 - Level 3, Lost is out!
July 16 : Alpha 0.4.1 - Fixed Weedle Evolution bug.
September 10 : Alpha 0.5 - Level Cap Raised to 20, New Level 4 Poison!
October 1 : Alpha 0.6 - New Level 5 Truth is out!
October 21 : Alpha 0.7 - Chapter 1 (real one) is out! New level 6 Journey, Level cap is 25, Ariados in Level Poison has less health, Magikarp, Bulbasaur and Staryu have spawn rates increased in level Truth.
November 18 : Alpha 0.8: - Added Mystery Gift and Pokemon Center buttons to the game. Pokemon Center available along with Mystery Gift now.
December 10 : Alpha 0.9 - Level 7 (Civil War) is now out! Level cap increased to 40!
January 7 : Alpha 1.0 - Level 8 (First Day) is out!
February 18 : Alpha 1.2 - Level 10 (Lessons) is out!
March 4 : Alpha 1.4 - New Secret added (Rescue), Music and Sound Effects added to Cutscenes.
March 25 : Alpha 1.5 - New Secret added (Truth). THERE IS A BUG WHERE IF YOU CATCH SLUGMA THE GAME WILL SUSPECT YOU OF HACKING. (Bug Fixed)
April 1 : Alpha 1.6 - New Chapter 2 Level Growth with a raised Level cap of 70.
April 15 : Alpha 1.7 - New Secret added (Growth), Bug fixes.
May 20 : Alpha 2.0 - New Level Proving added, Level cap raised to 80.
July 8 : Alpha 2.1 - New Level & Secret for Trial
July 22 : Alpha 2.2 - New Level for Chapter 3 Ghost Trial
August 19 : Alpha 2.3 - New Level Weather Trial, Level Cap increased to 100.
Next Update: N/A