I would also prefer the ending of Brotherhood as it had a more solid resolution, even though the original series was my first love of the franchise. I actually have both series box sets, as I feel that Brotherhood can be treated like a sequel even though it is actually a retelling of the adventure (manga point of view).
One of the last series I watched was Fullmetal Alchemist. It was gripping with moments of heavy emotion and tragedy, especially when Edward Elric temporarily died, but in all, a fantastic series (this show should still be highly regarded today).
This is my opinion in no particular order:
.Fullmetal Alchemist/Brotherhood
.Neon Genesis Evangelion
.Attack on Titan
.Death Note
.Akira
.Ghost in the Shell
.Cowboy Bebop
.Bleach
.Code Geass: Lelouch of the Rebellion
.Naruto/Shippuden
Two of the series I'm going to start watching are Cowboy Bebop and Sword Art Online. Plus I am going to see the re-release of Ghost in the Shell at a Cinema in Birmingham, UK.