Well this is my breakdown of the various Spiderweb Games series, I'll start with Geneforge. I could go on with even more information, but I'll try to keep it short as possible.
The Geneforge games don't have a continuing character file, but it more or less follows a continuing story of the Shaper civilization slowly losing control over their dominion by their own creations, by the end of the 3rd game a full on war breaks out.
The first two Geneforge games have the most freedom. In both, you feel like you're exploring the unknown and there are several factions you can help, join or destroy. You can even choose not to join any of them. I still think the second game was the best of the bunch.
The 3rd Geneforge game isn't terrible, but compared to the first two games, there is a lot less freedom. There are less factions to side with and its basically just "rebel" or "pro shaper" and not even much variation of those two sides and you'll have to pick a side eventually. I didn't care for the fact that they used an "agent" picture to represent the shapers in this one either, I prefer the faceless hooded shaper pics, but that's just me.
The 4th game sort of falls into the same less factions, pick a side category, but it's a bigger game with more places to explore and they try to do something slightly different by having you start out on the rebel side rather than the with the shapers. You can also play as a servile.
The 5th game sort of returns to having more freedom and more factions. You don't really start off aligned with anyone in this one though you're still going to have to pick a side eventually, but there is a lot more variation like returning things to the Shaper status quo, destroying the Shaper civilization, giving everyone equality, or going full creation genocide (rebel or not!).
Okay moving on to the Avernum (Which has games in the series that have been remade up to 3 times) and Avadon.
Again, neither one allows for character transferral, but they do more or less follow a continuing story.
Avernum in general is more "old school" because you create your party of four characters yourself in the beginning of the game. It also has A LOT more freedom of exploration, even more than Geneforge. There are just a ton of caves, lairs, cities and the like to explore.
This was even more true back when the original incarnation of Avernum was called Exile (Which I thought was a cooler name) because you could create six characters, had access to even more spells and the map was just so sprawling feeling. Think of something like Wasteland or Ultima 4, but A LOT bigger. (The Magic Candle would be the best association if you're familiar with that one)
Using a slightly more "recent example" party creation is like Icewind Dale, and you don't get any NPCs to join up. (At least you didn't in the old games, he might've changed it for the most recent remake)
Story and plot wise, Avernum is rather "meh" most of the time. The fun is found more in the exploration, getting loot and leveling up, so it's more like a Bethesda game in that respect. There's usually only one ending, but you can get variations on it based on a few major choices. The last game in the series probably had the biggest differences in that aspect.
Personally I thought the third game in the series was the best one. You got to explore a remote untamed part of the Empire in that one rather than just staying underground all the time. The second game of the series usually gets a lot of praise as well since that one involves an all out war with the Empire.
Basically the first three games in the series get more praise than the second "trilogy" but I thought the sixth one was okay. (4th one was pretty average and I never got around to the 5th game, but you play as the Empire in that one and I've heard people say it wasn't that great either)
Avadon feels more like a less graphic oriented version of the newer Bioware games minus their baffling obsession with romance plots. You get a set of NPCs that can help you and each one has their own quests at some point. You only get to bring two with you at any given time, but of course you can still go the entire game alone.
Avadon is definitely more story oriented, less freedom of exploration, but there is more than enough combat. The choices you can make are probably less meaningful than the ones you make in Geneforge. There's only one real major choice that makes a big difference in the endings. (You do get some variation on a couple of the minor ones though.)
So basically if you like Elder Scrolls better, go for Avernum.
If you liked Dragon Age/Mass Effect better, go for Avadon
If you liked both, well get them all!
