It's funny, I remember the bulk of old games as being overly complex without actually having deep gameplay, and that the bulk of the challenge was often in overcoming the UI. Not fun.
Now obviously there were plenty of gems in there, and there are some lost genres which I mourn with the rest of you and games I worry we may never see the like of again: X-Com*, Master of Magic, Magic Carpet, Tribes, Dungeon Keeper. However, I think in general memory is selective, and I'm glad to be rid of big clunky menus taking up most of the view, graphics you had to squint at, fiddling with autoexec.bat, and cassette-tape loading screens.
First heresy: Terror From the Deep was better than the original. Well it was the same, but harder and scarier with lobstermen, which makes it better. Hmm, does Dwarf Fortress have lobstermen yet? Gillmen? Aquatoids?
Talking of lost genres, consider Elite as an illustration of my prior point. The space-trading subgenre is all but lost. However, there is one pretender: the X series from Egosoft. And damnit it's too complex. The first three Elite games had plenty to do, sure, but they were definitely far simpler and the result was more interesting choices and more fun.
Second heresy: Civilization 4 is the best turn-based strategy game ever. The game mechanics are elegant and fit together beautifully. Seriously, I mean it: better than MoM, better than Alpha Centauri, better than chess.
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Dwarf Fortress is deep and complex and fun. I think perhaps because a lot of the complexity is not fiddliness for the player, but just fun detail in the game's system that produces chaos and variety. For example, I'm not really involved in which part of the body my dwarves are attacking beyond a general decision about what weapons to give them, but it's still cool when limbs get hacked off.