My favorite flop system of all time would be the Sega Master System. It was not actually a flop, though. It sold poorly in both the United States and Japan, the two biggest video game console markets (with combined sales of about 3 million), which were dominated at the time by Nintendo. The lack of sales made Sega bring the Mega Drive/Genesis to the market as early as 1988 in Japan.
However, the Master system was a success in Europe, with 6.8 million units sold. And it was a smash hit in Brazil, where it eventually sold 8 million units (over the course of 30 years), becoming the best-selling video game console ever in the country.
The Master System had a limited library, with most games made by Sega itself. But there were great games available for the console. Alex Kidd in Miracle World, Wonder Boy in Monster Land, Wonder Boy III: The Dragon's Trap, Castle of Illusion, Lucky Dime Caper, Asterix, Phantasy Star...