Before my response beings, let me clarify the point of the discussion:
To describe "Minecraft, done well."
This doesn't mean, how it should be done, or what difficulties Mojang or Notch would have to go throught to get there.
The idea of Minecraft done well, would be to have a feature-rich game, that is bug free as well as fun to play.

Now, I argue that several of the available mods are awesome and should be included by default.

You said,

"it is unrealistic and naive to program every mod."

If you didn't have a listening disability, you would realize that that earlier I said only the best should be included.
EVERY mod wouldn't make sense or be desirable. It should be obvious that only the best should be included.

"..instead, they need to focus on having a badass mod-support engine and API."

I don't disagree with this, I do think having an official ("badass") mod interface and API is a great idea. It would definitely be in alignment with "Minecraft, done well."

"I do think some current mods should be built-in, such as a way to see recipes so you don't have to rely on external sites for help. however, things like "pipes" are not necessary for the game to function and be fun. "

It's not about the game functioning. The game already "functions," so by that logic, the full version should be released and done. The game is also already "fun," again why not just quit working on the game? Oh yeah: the goal is to have minecraft done right, which means "feature rich."

On the topic of "feature rich," I remember a couple months ago your opinion of Minecraft, was that "Notch should stop adding food items and add more useful things instead."
Now your attitude is, "Notch should quit working on the game, and let mods to all the work."
I feel like Pipes would be that "something useful" that the game needs, and Mojang should implement.
A recipe book would only help you build the other same-ol-same-ol recipes, but pipes would add much more interesting value to the game and also increase fun.
(BTW, those kids at the pizza place were talking about the pipes mod ("Finite Water Mod"). Even those 12 year olds know better than you.. lololol )

" i would much rather have a stable stock game with less features ... than one with a ton of features, but buggy and nothing you can do about it because it's part of the stock game. "

This is perhaps the worst argument I've heard on the subject. We are talking about "Minecraft, done right." CLEARLY this means the final version having any bugs or stability issues is simply unacceptable. Your only evidence to base this pessimistic assumption is your experience playing a BETA. BETAs are obviously going to be buggy, and unstable. Your argument is invalid, because when I said these mods should be included stock, I never stated, said, or implied that they will harm or cause the game to be unstable in anyway. This is off topic completely, because stability is implied, if MC is "done right." I can't stress this enough: if Minecraft is "done right" why the fuck would it be buggy? Shows your lack of faith.

The argument that, if you don't like a feature you should be able to remove it from the game is insulting and petty. You can't play Portal, Assassins Creed, GTA III-IV, Plants vs Zombies, Braid, or anything other game and "Uninstall features you don't like." Thats basically saying "I don't like this game, fuck you developers." Clearly, if Minecraft is "done well," it wont have bugs and you'll have no need to remove features because they are buggy. Further, if any respectable game company, such as Nintendo, Rockstar, EA, Blizzard, etc., were to make a plain empty game and said "let the modders add features," they would be ridiculed for that bullshit.

Saying "that's what mods are for," is excusing Mojang for being lazy with their "eventually" attitude and excusing a "lack of features" for them.
We should NOT be excusing Mojang from THEIR WORK. I will repeat this later, slow people like repetition.
Ideally, MC should be feature rich, like you said: more useful items to build.
Although it's true that mods can offer more items, you have to understand business and the mind of the consumer to understand why mods aren't the solution.
(you're terrible at business and thinking about the consumer)

Consistency is extremely important for customers of all venues. This is why most Costcos are laid out extremely similarly. This is why every Best Buy looks damn identical inside. This is why EVERY In'N'Out is exactly the same. People like consistancy, and feel safe in a known environment. Video Games are no exception. The stock minecraft should be consistent and feature rich, so every vanilla player has a great experience.

If you download and install MC at home, then play at a friends house and its completely different the experience will be frustrating and disorienting. Further, if you become accustom to building certain items at your friends house, it will be equally annoying when those things do not work at home or elsewhere. It makes it hard to write strategy guides or discuss the game publicly because everyone will have a different experience. The entropy will taint the culture. You must understand that not everyone is a hacker, or even teenager. Some players of minecraft require their parents to install it and run it for them. No matter how "easy" it is, the technicality of installing mods is more than should be expected of any user. Even if its just downloading a zip or a jar and putting it in a folder. A LOT of children and adults will stumble trying to find %appdata%. I know neither of my parents could. Requiring mods for cool features should NOT be the case. The cool features should be default, so everyone who plays, can have the best possible experience. Would it kill you if pipes were added? What about rideable horses? The "best possible experience" shouldn't depend on the player. It's the JOB of Mojang to create the "best possible experience." And to do so, the game ought to be feature-rich as possible. As mentioned above, clearly it should be stable regardless of features.

On the subject of Notch and Jeb being able to complete the task of including the mods stock:
Mojang is worth $20 million.
Notch could higher 20 full time programmers (40hrs/week), and pay them $20 per hour, full time, for six months and only spend 38K.
Thats about a third of one of his 20 millions.

Mojang has the time, and resources to program every (important) mod natively, and get it "done right."
Native programming runs better than third party mods, and it would always be server compatible.

Even if you add more programmers, if a game like GTA can have hundreds of engineers working together, to make an IMENSLY, FEATURE RICH game, I'm SURE notch can handle 20 guys.

Whats more: Assuming Notch & the gang implement a mod API, all future updates to the game could use this framework (internally, inside Java.) Meaning anyone who is assigned to implement a particular mod or feature, would be able to work completely independently of the rest of the team. However these points are moot, since the topic is "Getting MC done well." It doesn't matter what path, strategy, money, or breakfast tea Mojang uses to complete the job. So trying to defend Notch by saying its too much work for him, is silly.

Now to recap:

It would not be difficult at all to include "only the best" mods. I never said anything about including "all" mods, so you better check-yourself about who is "naive."

Good games, such as GTA, Roller Coaster Tycoon, & Others are Feature Rich, when they are Stock. Minecraft should be no exception.

Notch has the money and time to make sure Minecraft Final is "done right," without bugs and a great selection of items, powers and abilities in game.

This argument was never about whether or not Notch could do this by himself, or how difficult it would be for Mojang, but even if it was - I've shown how it would actually be very easy.

Consistency is extremely important for players. If you think all the cool features of MC should be mods, you have no clue about good game design and satisfying customers.

Final thought:

"also, notice that none of my words are capitalized. this is because i am an adult and don't need to shout a billion lines of capitalized text to make me feel like i've gotten my point across."

Anyone who isn't a fucking retard would know that talking via text is ALOT less emotional than talking in person. Sometimes, emphasis is required to express the importance of certain items. During this response I've used CAPS less, but I used bold and italics to make sure readers will correctly understand my points. Using caps on AIM is the easiest way to express emphasis, because selecting text and choosing bold / italic can be a PITA. It has nothing to do with being an "adult."
But speaking of being an adult, you might want to try it sometime, here are some tips:

Don't repeat the same argument 10 times after it's already been shown to be incorrect. (Defending Notch is off topic, yet you keep telling me how hard it would be for him to program...)

Read what the other person types. (Seriously, are you reading this?)

COMPREHEND what the other person types.

Some people are slow readers / thinkers, re-read it and spend extra time to analyze it if you need to.

Don't blurt out the first response that comes to your head, this makes you sound stupid and eventually will be proven wrong.

Don't make assumptions (such as Minecraft Final would be buggy). "When you ASSUME makes an ASS out of U and ME" -9th Grade Physics Teacher.

As long as you adhere to these rules, chances are the other people wont have a need to use bold, italic, or CAPS.

In closing:

Saying "that's what mods are for," is excusing Mojang for being lazy with their "eventually" attitude and excusing a "lack of features" for them.
We should NOT be excusing Mojang from THEIR WORK.