The PCE Popful Mail is a completely different game than the Sega/Mega-CD version. The story is similar, but that pretty much it.
Comparing them as games is like comparing Legacy of the Wizard to Dragon Slayer Turbo CD.
They're both great and both have very nice graphics, but each game's visuals have different strengths. I prefer the vibrant colorful PCE graphics that feels more like a console game. The Sega version is like an arcade adventure game.
The Sega version has nice fully animated cinemas, but the PCE version's character art is touched up very nice. They both have lots of nice bonus touches that make each feel like the developers took the time to really polish them instead of resorting to shovel ware.
The Sega version definitely makes much better use of its console's hardware, in the 'tech demo' sense.
I don't think that either game is too expensive now, so anyone who enjoys adventurey games should get both.