Well, that's the thing, the name indies didn't exist, Doom had a normal sized team for the times. Doom was released under the Shareware model, meaning the first of three episodes could everyone copy for free and include on discs on magazines (remember, internet wasn't a thing everyone had back then). For Doom the shareware version contained the first of three episodes. At the end you got this message:

That was pretty usual, about a third of the game as shareware for free copying, so that the game reached a lot of people and paying for the full version. This often involved mailing actual money bills inside a letter and getting a disk back the same way.

Doom was self-published (Doom 2 got another publisher and released without shareware as boxed version), but prior id games including Wolfenstein 3D had one of the biggest publishers at the time: Apogee Software. So was it any less "indie"? Well Apogee also released their games via the shareware model and Apogee at the time were like 10 people. So also indie after todays standards. Because pretty much every game was indie if we apply modern standards. Lot's of the "big" game publishers operated from the garage of private homes. Because gaming was so niche back then.

And that is why todays indies still have it better todays than all game devs in the 90s, as you noted. They can reach a lot of customers via digital distribution. Payment these days can be made via online payment options, not mailed in a letters as dollar bills.

Well this is just not true.  Just today I was looking for Marvel Ultimate Alliance 1 and 2 for PC.  Go ahead.  See if you can find them digitally anywhere.  You can't.  They have been removed from Steam and every other store.

Ubisoft has already delisting a couple of games, and more are coming very soon.

It can happens but it's rare. With physical it's the opposite, the standard is to not find the game to purchase if they go out of print. Only the popular ones are easy to find and even then you'd likely have to buy them second hand 

Remember not every country is huge for consoles like Japan where people throw their old games in the trash can on weekly basis 

Well this is just not true.  Just today I was looking for Marvel Ultimate Alliance 1 and 2 for PC.  Go ahead.  See if you can find them digitally anywhere.  You can't.  They have been removed from Steam and every other store.

Ubisoft has already delisting a couple of games, and more are coming very soon.

Nope, never heard of shareware, shown how much indies are willing to use it nowadays. For indie developers digital distribution is a Gods send, much easier to release and distributed their games worldwide. That's why so many games were never released outside some markets in past (many never released outside Japan)

I'm perplexed that you listed using big publishers (at risk of losing their legal rights) as a truly viable way to publishing. Seems something hard to hear if you're a small developer. 

From those games I know Doom and Wolfstein, which I'm surprised to discover to be indies. 

A lot of these terms didn't really exist at the time, but there were similar things going on.  No one used the term "indie", but Doom was self-published.  No one used the term "free-to-play", because they said "shareware" instead.  But shareware was a way to get a whole lot of people to try the game for free knowing that a small percentage would buy the game.  (Demo is not quite the right word either, because 3 levels of Doom is more than what most people get to play in a demo.)  We also didn't have the word "causal", but that was my impression of the people who really liked Doom and other FPS games.  My buddy kept going on about how great a game Doom was, but I didn't think the game was too special.  I realized he never went to the arcade and the only console game he ever played was Tetris.  That is why he liked Doom.  Damn casual.

Of course, I was just an ignorant "hardcore gamer" at the time.  Now I realize that gaming needs casual gamers.  That is often how new genres become popular.  I saw the same thing happen to MMOs with World of Warcraft.  It was a game for "filthy unwashed casuals".   But if casual gamers play games for long enough then they become hardcore.  And they often need to try a game for free or for cheap, because they aren't that invested in gaming to begin with.  That's how the FPS genre started.  Doom became popular, because a bunch of casuals tried the game for free.

It is less rare than you think.

https://delistedgames.com/

Are you aware this list includes delisted games because other versions are released, right? (ex: Dragon Quest XI) Sometimes the game even gets a new launcher because of publishing issues (ex: Fall Guys). This is indeed a great website because it provides us the reason why the game was delisted

But I agree it can lead to shady practices, like Nintendo removing Tropical Freeze from Wii U store, so people needed buy they more expensive Switch version