Similarly if you look at any other series:
- Age of Kings was clearly Age of Empires version 2
- DOOM 2 was clearly DOOM 1 version 2, DOOM 3 was clearly DOOM 2 version 2
- Caesar 2 was clearly Caesar 1 version 2, Caesar 3 was clearly Caesar 2 version 2, Caesar 4 was clearly Caesar 3 version 2
But I disagree here, AoK is quite different from AoE. Its not just a graphical update, there are many things in AoK that work differently than AoE. For example, AoK has much more early defenses, and more powerful defenses throughout the game. Rushing an other player early is no longer a good option.
DOOM is not a good example, it is an FPS, and all FPS play the same; you shoot at everything that move.
I never played Caesar so I can't comment on it.
I can talk about SimCity, SC3 and SC4 are also very different, there are many things that you must do different in SC4 to build a succesful city. For example, in SC3 you could start with zoning medium density zones right away to quickly make a relatively large city with a good income. In SC4 light zones at the start actually earn you more, as the price will go up over time, you can change it to higher densities at later times.
An other example is Diablo, Diablo 2 plays much more like an arcade game with its huge amounts of enemies that can be battled at the same time. The fact that the game is also much larger and it takes longer to get to the end also makes it a completely different experience. Not to mention the completely different skill sets for each character, while in Diablo each character had the same spellbook, but only different abilities to maximize the use of bows/melee/spells.
I feel the differences between Civ3 and Civ4 fall in line with it. It would have been worse if they made Civ3 version 2, then we could have complained that the game industry never invents something new and is just milking old concepts with fancier graphics.
Really, there can be only so many variations of Tetris before they start to look like Yet an other Tetris clone. (YAOTC)