1) Lust 2) Greed 3) Hughes 4) Mustang 5) Maria Ross 6) Sloth 7) Winry 8) Izumi 9) Shou tucker 10) Rose 11) The Elric brothers 12) Envy 13) Scar
Characters FMA:B does better
1) Bradley 2) Mira Armstrong(is not even in FMA) 3) Kimblee 4) Hoenheim (barely) 5) Armstrong (barely)
The Chimeras in fmab are given a bit more screen time fmab but felt more tragic in 2003.
For characters that aren't directly comparable. 2003 Wrath > FMAB Pride. Dante > father (mainly because she wanted fuck Ed and also BTFO his ideals about Equivalent exchange).
FMA 2003 has better overall OST(only The intrepid from FMAB is memorable) and their OPs and EDs are about equal. 2003 has less grating humor and a better overall visual aesthetic. FMAB has more but not necessarily better action. Thematically 2003 is better as well. Ling was annoying and ruined greed but Mira Armstrong was a nice addition in FMAB.