RPG maker can do what you’re describing quite easily with 'fork events'. As for which RPG Maker program to use, it depends how much programming you know. RPG Maker XP is the most recent version, but it's very inflexible if you don't know how to edit scripts with Ruby. RPG Maker 2003 may be the better choice in this case, which has more pre-set event commands to choose from.

Really though, 2003 is geared more towards FF type games (it comes with an ATB battle system) where as XP is geared towards Dragon Quest type games. I've never seen someone try to make a traditional CRPG like Baldur’s Gate, but I'm sure it's possible. You're pretty much SOL if you want to make a battle system like BG in 2003 though; you definitely need to use the Ruby scripting in XP for that sort of thing.