I just completed Avernum the other day and started Geneforge soon after (am just outside the third settlement having cleared everything south of the northern grindlands) and so far I am the opposite to you CL, I much prefer the Avernum format so far. Where Avernum gives me that classic D&Dish vibe, albeit without the factions element so much, Geneforge seems much more of an adventure-game-RPG-hybrid feeling. There are things I prefer in Geneforge, such as fast travel, Avernum's weakest aspect being all the forced running around for infinity and beyond, but, overall, Geneforge seems to have quite basic gameplay in a more interesting story whereas Avernum has more traditional gameplay in a less interesting story.
My biggest immediate disappointment with Geneforge was when a screen popped up saying "you can only have 3 different types of creations at one time" for 7 slots. Well... that's a bumhole. Here you are with a game where you can have one of the most fun group dynamics in cRPGs and 8, yes, an 8 team party... but they all have to be the same creatures? So if I want to upgrade my Fyoar (sp?) to a cryoar (sp?) I have to delete my Fyoar that I've already spent 10 levels levelling up? Well that fucks up the whole point of levelling them up doesn't it. Also, the stats are way more obtuse than Avernum as you really do have an interest in all the skills what with it being a single character game (none of your other potential 7 team posse members can do anything skillwise beyond main stats), meaning that, if you want to clear that bridge of mines you have to have XYZ mechanics skill (or permanently lug around 5 billion living tools which make my mage encumbered in a nano-second), a stat I shouldn't be investing in as a mage class. ie: most of my skills are convenience buys rather than upgrade buys.
Geneforge is also a lot weaker at telling you crucial stats and other information. For example, when I had the ugly C&C choice of whether to absorb my older creation I tried to find out exactly how much essence it was currently consuming, but not a single word of this exists anywhere. Nowhere does it tell you how much essence each creation is currently costing. Also, rather crucially, I have no idea, and the game doesn't tell you, even in the game-wiki, whether Dexterity is needed for missile spells like firebolt, spell crystals or wands to have a better chance of hitting their target?. Likewise, do the magical attacks of the magical creations require Dexterity to have a better chance of hitting? My main character has very good Firebolt skill (4), very good Battle Magic (5 I thing) and has Intelligence of 10 but his Firebolts have the least chance of hitting their target than any of the newly created creations. Also, all the creations have uniform starting stats, like 7-9 in all base stats as soon as you summon them, but you still need to give them 2 Intelligence to control them, no matter what their summoned stat is, and yet my main character's main stats are, like, 2, 2, 10, 2 and I'm wondering why my shaper has such shit stats when he can so easily summon flat 9s out of thin air.
Also, in Avernum you can avoid respawns outside of caves and structures and inside cave structures it's normally inconsequential respawns, but in Geneforge the respawns will just keep at the same consistency no matter how many you 'clear' before going back (unless this is a specific feature of the northern grind areas for grinding's sake?). Whatever the reason is, Geneforge tires me out and provides less hours of playtime per session than Avernum did. I could play Avernum until I was literally physically fatigued. With Geneforge mental fatigue kicks in well before the physical fatigue.
Ah shit, that turned into a right ugly wall of text.