Pixelmon is a very popular Minecraft mod. It basically implements Pokemon into Minecraft, removing a lot of the Minecrafty elements for convenience of finding, catching and training your team. Of course, it is a mod and quite a sizeable one at that. So what do you do if you're no good at modding Minecraft? Play a map of course.
Made for vanilla Minecraft 1.8.8, Pokemon Cobalt and Amethyst is a map that makes use of command blocks and was built by a team of players. The project took them about a year and a half to make and was based around trying to replicate things as they were back in the original game of 1996 - although in an original region (Suliqu) with unique stories and 136 new Pokemon that mixes in a few of the later gen Pokemon with the originals. It is however only available in singleplayer right now, so no link cable simulation I'm afraid.
Developer Phoenix SC claims that the game has a playtime of about 60-80 hours and features "an antagonist threatening to release a legendary darkness that demands tribute." The criminal team in this game won't be Team Rocket, Magma, Galactic or any of the other gangs from the official games - this time they're Team Tempest.
Of course, fan-made content is wonderful but Nintendo have a reputation of stamping out the more popular and noticeable fan-made creations. Pokemon Uranium was one of the biggest to fall, only last year after fans spent hours on its development. Cobalt and Amethyst do make use of sounds borrowed from Red and Blue as well as other assets so it remains to be seen whether Cobalt and Amethyst will avoid the DMCA takedowns.
If you're interested in playing Pokémon Cobalt and Amethyst for yourself, you can download the map here. See the video below about how to install it if you're unsure: