Geneforge is the best series overall. Unfortunately your choices don't really matter because nothing carries over to the next game, Jeff has already decided on a canonical ending for each game except for the last one. Avadon has the same problem. Kind of makes me wonder why he bothered to design his games this way.
The Avernum series is good if you're into adventuring games but it doesn't have any of the moral dilemmas or choosing a faction that Geneforge or Avadon has. Avernum 1-2 are good but the games are basically a giant scavenger hunt that drags on for too long. Avernum 3 is the best in the series. The gameplay drastically changes starting with 4 and the series becomes much more grindy and less flexible.
Also the remakes of 1-3 are shit. Avernum 1-3 are open-world and the gameplay supports that by letting you go to dangerous places before you're strong enough, possibly to do a quest or to find a good piece of equipment, and if you're careful, you might survive. The remakes give you the illusion of an open world but going out the expected main quest path will get you killed by a random encounter before you can even make a move. It adds a few things that weren't in the original but nothing really important or interesting.