You've only played the first two games (which were, indeed, good). But There was a third Master of Orion game which bombed badly, most likely due to the excessive level of automation in the game. I have a copy of MoO3 and from what I remember (i haven't played it in a while because it sucked) trying to get any measure of real control over the game was almost like trying to wrest control of a spaceship away from the HAL9000 in that the only way I was able to figure out to idsable the AI's belligetrent overrides was to just turn the damn thing off...
I believe he was making a point of saying "There was no MOO3".
Anyway, to follow up forsaken1111's point...
The critical design failure of MOO3 (as opposed to accidental bugs, I mean the "they simply did not plan the game right" type of failure) was that there WASN'T automation for some things that really could have used it.
The only serious "knob" you have to play with (aside from picking a new buildling to add into your planet or the like) was a "tripod" that was the bane of the game. Every planet had a balance of spending for three things (I think it was science, domestic, and military spending), and adding funding to one made everything else less efficient, meaning you had to constantly fiddle with these sliders to pixel-hunt for an ideal balance of spending to maximize your growth potential.
For every planet you controlled.
Every turn.
And this game can have up to a hundred planets under your control, and last a hundred turns or so.
If that were automated, it would have taken the single biggest reason people HATED the game out of the picture - but then, it wouldn't have had much left inside of it, either.
And then there were the balance issues, like the "Gas Gods" living on Jupiter-like planets that give them massively more building space than other races, plus giving them the bonus to population growth on top of that, ensuring that they grow two or three times faster than anyone else in a game that is entirely about how quickly you can grow your empire. Yeah, fair.
Oh, and if we're talking about AI, another of the crippling failures of that game was the droolingly stupid AI. Including an insect race that was so random in diplomacy that it would want to sign an alliance with you on the first turn you met them, then declare war the very next turn, then sue for peace the turn after. Did I mention they would do this before they even knew where your planets were, and all you ever had was scout ship to scout ship contact?
If Toady wants to make a better AI, that is most certainly not wasted time. Whether it is making dwarves less suicidal and more aware of their surroundings, or making town villagers capable of reacting to events in a more lifelike fashion, or just making random monsters more clever and dangerous predators, then it would only improve the game.
If Toady wants to give players the ability to automate some routine tasks, it will almost certainly be of benefit to the player. Any task that is so mundane and routine that a player will want to automate it (like, say, making sure that stills are always making more booze, even if they ran out of barrels at one point) is probably something so boring and tedius that the player will probably not miss having to do that sort of thing when it's gone.
Any task that a player can trust a computer script to do for him correctly every single time because its problem and the tasks taken to solve it are so clear-cut and routine as to never need any further thought than a simple "If, then" response is one that probably shouldn't be asked of the player in the first place.
When games actually DO automate tasks, you can tell whether the game had a real concept behind it in the first place because there will still be something left for the player to enjoy doing.
MOO3 was such a terrible 4X game because if you got past the micromanagement, there wasn't even that much left in the game for you to do.
Final Fantasy XII had a combat system so simple that once they gave you the ability to script 12 if-then commands, you could literally run the game on autopilot, only needing to guide the character from fight to fight by the left analog stick. There was even a particular enemy you could go all the way up to level 99 on (taking three days to do it, though) because it summoned an infinite number of enemies to fight you, and you could kill those enemies for experience while avoiding harming the boss monster. Oh, right, and in case that exploit wasn't enough, they purposefully put in a monster with 8 million hit points that takes several hours to defeat, and where there's pretty much nothing you can do but set up a script to do the battle for you, and go to bed.
A well-designed game will not pad itself with needless micromanagement, and will take care of the tedious busy-work for the player so that they can focus on the more enjoyable, dynamic aspects of the game.
Hence, something fairly simple, like just keeping the stills producing booze because you didn't notice a job cancellation alert a season ago are perfectly fine because there will still be something in DF for players to actually be able to do.