I have seen iterations of this thread many times and I'll say what I always do:
In terms of US only releases, I feel like the SegaCD has a better library.
But in terms of a global or even Japananese only market, the PCE CD family is the clear leader.
In Japan the MegaDrive was nowhere near as popular, and the devs and amount of money and time spent on producing titles for it pales in comparison to what was put into the PCE CD. I love them both and play and collect for them both, and both have some excellent exclusive titles too.