In a market of non-differentiated products, the company with the most clout brought to bear wins. That's exactly what happens in the JRPG market. Most are nearly or entirely identical, meaning that the ones that stand out due to reputation or excessive advertising (such as Final Fantasy and Dragon Quest) end up dominating the market. I can't count how many JRPGs there are out there that can be summed up as "Dragon Quest clone". They were everywhere on Famicom and Super Famicom, though the copycats have stopped being so prevalent over the last decade or so.
If any RPG developer hopes to overcome Square-Enix, they need to do something that no RPG developer (save perhaps the Pokemon developer) has the guts to do: target non-RPG players. Ideally, by removing elements that make most not want to play RPGs while adding elements that RPGs lack which would make them more appealing to non-players and current players alike. As long as the genre remains as it is, its market won't expand and companies won't be able to defeat the industry juggernauts.