The following is a quote from a Hiromichi Tanaka, taken from the liner notes of the Seiken Densetsu Music Complete Book compilation (a compilation of all Mana soundtracks, released in 2011 for the Mana series's 20th anniversary):
[...]upon getting word from Nintendo that they were developing a CD-ROM adapter for the Super Famicom, we decided to start a project in a different direction from Final Fantasy IV, which at the time was in the middle of development and was touted as a next-generation RPG fitting the large storage capacity the new cartridges had. The development codename for the new project was Maru Island, and we were making it as a collaboration work with Akira Toriyama-sensei after we established contact through Shueisha. I frequently ran back to the office just to receive and look at the screen mock-ups that Toriyama-sensei did in the initial stages of the project.
Despite that, the CD-ROM adapter was never completed. Once everyone learned that the CD-ROM adapter was never going to see a release, they decided to abandon everything that had been planned for development since the very start, including Toriyama-sensei's contributions, and decided to revise the project in order to make it release into a ROM cassette. We said that we would wait for the CD-ROM to make a collaboration project with Toriyama-sensei, but when it was revised, it actually became an entirely different project with an entirely different direction. That was what later on was completed into the game we know as Chrono Trigger.
Thanks to the high speed of the ROM, it was possible to seamlessly make the action visible in the field without the need to make a transition into a battle screen. But in the end, the new RPG I wanted to start making — one that didn't have a command-style battle system (Motion Battle System) and tested the reflexes of the players — wasn't a title that existed at the moment.
Upon seeing that my goal was to make an action RPG, and learning that an ARPG was the next game we were going to make, I decided to make it into a sequel for Seiken Densetsu, so we reestructured everything to use the world setting we had already from the previous game, and Seiken Densetsu 2 was finally completed.
tl;dr: Squaresoft wanted to do an RPG with Akira Toriyama for the SNES Super CD-ROM add-on, but Nintendo canceled the Super CD-ROM, so the failed project became two new, distinct games instead: Secret of Mana and Chrono Trigger.
Source: http://www.squareenixmusic.com/features/liners/seikendensetsubox.shtml --- http://tinyurl.com/6ak2wg8 ^Almost all non-translated FF Ultimania interviews ever. Tons of exclusive info. Please help translate them.