Honestly I don't think you are getting very good advice. Did you see my Geneforge 3 thread? If you only plan on playing one of them, start with that. As far as puzzles there are several challenges that play to certain strengths, which is a puzzle. For example, (without spoilers), there might be a room with a boss and some other potent enemies that can be disabled if you are clever instead of simply charging in. Minefields. Spawners. Pilons. Poison fields. Enemies with unique characteristics that are themselves a puzzle. There are tons of them especially in the later games such as 3, 4 and 5.
Geneforge 1 has factions but is otherwise a pretty crude example of where the series ends up developing to. Stories, creative areas including puzzles, crafting, enchantment etc.