Not much to add that hasn't been said, but while Avernum does have choices that you make, and that may affect the ending, they are either relatively minor, or very late in the game, meaning that the game is identical for the first 80% (disclaimer: I have only played A5 and a bit of A1 and 3). Geneforge, on the other hand, is far more open ended. The game is vastly different if you make even the slightest different choice. It is, IMO, much more engaging. The morality in pretty much grey vs. dark grey vs. darker grey vs. black- there are no "good guys" in Geneforge. The characters are much deeper, and the potential for complex moral and philosophical issues is greater. Just look at all the canisters or shaper v. rebel or creation rights threads in Geneforge, compared to the much more gameplay oriented threads in the Avernum forum. Also, the creation system add a whole new dimension to the game (again, the amount of time spent discussing Drayk vs Eyebeast vs War Trall is fascinating, and the calculations each side makes to back it up are impressive), and nicely compliments the dark setting by adding a not-so-simple question of what is human and what is not. Geneforge torment character building is an art unlike any other, compared to Avernum, where the difference between picking the premade party and a custom party is helpful, but not game breaking, where in Geneforge, you mus push the engine to its breaking point.
To summarize:
PROS:
Geneforge has plot, depth, choices, and a more interesting, although more complex, system of combat and magic. It also has nicer-looking graphics (than A1-3, at least)
Avernum has a streamlined simplicity to it that many RPG's like. It also has a much more stark contrast between the two sides. Cookie-cutter morality is also popular amongst many gamers.
CONS:
Geneforge's real-time movement can be annoying at times, since in Avernum you can exit combat mode, save, and reenter, while in Geneforge, you have to exitsaveenter to avoid taking tons of damage from the level which gives you 100 points electricity damage per second. It is also, IMO, more difficult at higher levels. Plot can get repetitive, though (OMG. Shapers v Rebels. And someone thinks the war is stupid. Great.)
Avernum 1-3 has bad graphics. Most people won't like them. Some do, but most are so used to 3d photorealistic graphics, this may be a turn-off. I found Avernum also rather tiresome, plot-wise, and I dislike the whole Empire vs Avernum.
Click to reveal..
The Vanhanti I loathed. They were a poor plot device initiated because Jeff was too lazy to think up a way for Avernum to not get their asses kicked by the Imperial army without turning to alien saviors. What is this, Star Wars? Oh, and they are overused in BoA, too.
Really, do you prefer a standard RPG, with a little twist (Avernum), or something much, much different (Geneforge). The choice is yours.