While I'm not going to disagree with you, phatoalpha, I might suggest a different example from Morrowind's host of flaws. The Alchemy issue is a flaw in the system that a power-gamer can exploit, but such loopholes are going to exist in any system. Sit a power-gamer down with any edition of any RPG system, and given time, he'll find something.
Morrowind's journal system is something that not only saps the fun from the game, but does so for everyone. I've made four or five attempts to finish Morrowind, now, but haven't reached the central plot's conclusion. Why? The first four times, I decided to do some sidequests, and because the journal system fails so miserably at intuitively tracking quests, I lost the plot entirely. The last time, I was doing just dandy at keeping track of the main quest, by avoiding nearly all side-quests (which really seems to sap the game's potential, but I would like to finish the damn thing), but when I took a break from the game for a couple months, I couldn't drop myself back into the plot straight away, again, because of the awful journal system.
I could gripe about the combat system being too simplistic as well, but everybody knows that. You can't do a one-to-one port to PC, from a console, and have an intricate, yet intuitive combat system. This is something else that concerns me about seeing Fallout 3 being designed both for consoles and with a real-time combat system. Under a turn-based system, even if the console controls are a little clunky, the player would have time to cope with any difficulties inherent to using a game pad, versus a mouse and keyboard. If the game was a PC-exclusive, the combat system could still retain some of its former detail, even in a real-time environment (given reasonable pacing), since so many controls are right at the player's fingertips.
Oh well.... I'll probably have a year's worth of buzz to read by the time I actually get Fallout 3, anyway, since it or Spore will likely require substantial hardware upgrades on my end. May as well wait for Spore (now tenatively slated for '09) and pick both up at the same time, while simultaneously clearing my calandar for the next eighteen months.