sega lost their bottomless pits of yakuza cash in the late '90s and slowly all their talented developers left.
they also made a lot of games based on time-limited property licenses like daytona and ferrari that makes re-releasing them and continuing to make money difficult.
for example, daytona usa is only "daytona usa" because the offices of the simulation department of martin-marietta, the company that actually built the model 2 hardware, was at the time across the street from the racetrack, they never actually acquired any license from the track to use the name until much later when they were nearly sued. same is true for the ferrari in outrun.
their other games have licensed music or character designs like crazy taxi and virtual-on and even more problematic, many games' source code was just completely lost. the guy who made the M2 emulator is the only reason you can play console ports of some of Sega's old games right now.