In theory it could be done, easily, by finding the XNB file that houses the music. Extract it to find out song titles. Once you know the song titles you could make a new XNB file to replace the old music one, by packaging up pokemon songs with the same titles as the regular Stardew Valley music files. Of course there's probably a better way, but this would be fairly easy to do if you know how to install and use xnb_node. Be sure to use the same file format for the pokemon sound files. I'm unsure if different song lengths would be an issue. I can't think of a reason they would be... but back in my Skyrim days it was an issue.
It's not like the graphics edits, you have to edit the Wave Bank.xwb file. You'll need a few programs; unxwb and MediaCoder. Unxwb unzips the Wave Bank.xwb into Wav files. Just convert a song want, and rename it the same as the song you wish to replace. I'm searching for a program to repack it.
SOUND\MUSIC MODDING GUIDE for v1.05+ UPDATED 3/14/16 ? Also here's a quick and dirty guide to sound/music modding, its similar to terraria. I have created a tools pack for easy install. 1. Download the Direct X Software Kit Here. When installing, do a custom install and ONLY choose to install the "XACT" software. 2. Download my SOUND TOOLS package (new for 1.05) at the bottom of this post. 3. Extract WaveBankExtractPackv2.zip somewhere where you have lots of space. The unzipped game sounds take almost 1.3 GB of space. We'll refer to this location as your Work Directory. 4. Copy Stardew Valley\Content\XACT\Wave Bank.xwb to your work directory. 5. Run "Extract Wave Bank.bat" in your work directory and it should extract all the files to the "NEW" folder, while automatically encoding them to a file format the XACT application can use. 6. At this point, the Work Directory\New folder will contain every sound and music from the game in .WAV format. Keep in mind currently you can ONLY replace existing .wav files, you cannot add your own. Use a program like Audacity (or any sound editing software) to modify or save any sounds over the current ones - remembering to save as "16bit wav file" audio. Keep in mind no matter what you do, the only way to get your sound/music in-game is to replace an EXISTING sound. 7. Once your files are replaced/modified, its time to compile. With XACT already installed, go to your Work Directory and open NEW\NEW.xap and it should already open the project ready to go in XACT. 8. However, you will need to update the path to point to where YOU have your sounds unzipped - the NEW folder step 3 created. 9. Double click "Wave Bank" on the left so it shows a list of all the files on the right. Highlight them all, then right click and choose "Update Source Path". [?IMG] When asked for the new path choose the \NEW directory the sounds were extracted to. This will update the locations to match your computer. Verify it shows 355 sounds on the bottom left of the sound-list window. NOTE: People are reporting this may duplicate the listing of every file so it will show 710 files in total not 355. If this is the case, make sure you delete the duplicates! The first file listed should be 0000000.wav and the last one must be 00000162.wav. Exact order matters 10. To compile , go to File > Build. The compiled sound package will be in the the Work Directory\New\Win folder, named "Wave bank.xwb" 11. Copy it back to the Stardew Valley\Content\XACT (making sure to back up your old copy first) and start the game. 12. You will learn very quickly if it worked or not. You should first hear birds chirping, followed by the main menu music once it shows the pink birds flying past the mountain. If you do NOT hear this, the order is wrong and the sounds have not been compiled correctly