(Thank you to EliGamerX for dumping this and documenting the differences!)
What's Different from the Original 1996 Release? (Disc Contents)

In the Disc's Files
*The following folders have been removed:
**The DDCHK folder, which contained DDRAW.DLL.
**The MOVIE folder, which contained PUYOTECH.AVI, a video where two "Puyo Masters" from the Bayoen Tour '96, Hiroo Tanaka and Teruhisa Yoshikane, play three matches where they showcase some high-level playing techniques.
**The PUYOBMP folder, which contained 35 bonus Puyo Puyo and Madou Monogatari bitmap images.
*The following folders have been added:
**HTML, which contains a webpage for troubleshooting issues with the game.
**OMAKE, which contains:
***The "Version B" Windows demo version of Guru Logi Champ for GBA (which was also distributed separately alongside the below extras on its disc), as well as an HTML manual and folder for images used in said manual.
***The TV commercial and official website for for Zanac X Zanac for PS1.
***The web version of the catalog for Compile's "Puyoman Honpo Momomo Mail Order" mail order service that offered various Compile products, mainly licensed Puyo Puyo and Madou Monogatari merchandise.
*The DirectX related files in the root of the disk have been removed, and PC-98 specific drivers are not included as NEC had mostly phased the line out by the time this release came out.
*The version of DirectX included on the disc has been changed from DirectX 2.0a to DirectX 8.0.

In-Game Changes (Note that some of these changes also apply to the 1999 DigiCube rerelease of the Windows version of Tsu, but that version is currently unavailable for checking)
*The "Act Against AIDS" logo on the Compile screen has been removed (with the Compile logo being moved to roughly the center of the screen as a result), and the section of the Options menu that explains what Act Against AIDS does was removed.
*The Compile copyrights on the title screen and in the credits were changed from "©COMPILE 1994/1996" to "Developed by COMPILE 1996 ©SEGA CORPORATION".

Other Notes
*The installer program now runs under newer Windows versions. Japanese fonts will not display correctly unless the non-Unicode language is set to Japanese or Locale Emulator is used.
*Like the original 1996 PC release, the game is DRM-free and can be run without the disc once installed.