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When the Yogscast started their Minecraft series (speaking only about the main episodes, not the side episodes like the mod spotlights), it was created as a Let's Play of Minecraft (complete with showing how to survive the first night). It eventually evolved into one of the most well-produced machinima series ever made.
Also, Lewis had never played the game before, so Simon did most of the work. After Lewis became more familiar with the game, the role was flipped, and Lewis usually took charge.
The first season of Red vs. Blue had the cast use voice filters to try and simulate the effects of helmets on their speech. This was removed in the second season since it made it difficult for viewers to understand them.
Church originally was a ghost rather than an AI, so early on, especially before they decided to actually go beyond about 10 or so episodes (which was the original plan), Church was capable of doing things that he could not do in later seasons.
Grif commonly tells Simmons that they should get back to work and focus on their tasks in the early episodes. The Grif of the later seasons is anything but concerned about tasks, reveling his status as team slacker. He also is later claimed to be the sole draftee of the Red and Blue armies, but in the first episode claimed to have "signed on to fight some aliens".
Sarge had a voice akin to R. Lee Ermey initially, but his voice actor Matt Hullum found it too hard to keep doing, so he traded it in for a stereotypical Texan accent.
Caboose was just kinda dim when he was first introduced, not the completely divorced from reality character he is today. Midway through Season 1, his intelligence began dropping in chunks between episodes, and has never come back. Word of God is that being possessed by O'Malley then having him being forcibly ejected left a detrimental impact on Caboose's head.
Donut was just a red counterpart to Caboose, also being vaguely dim. He also objected to his pink armor, calling it "lightish red". Once Season 2 came, the writers decided they couldn't get much material out of that angle anymore, and instead made him a flamboyantly over the top Camp Gay character.
Master Chief is actually mentioned in the first episode—him "blowing up the whole Covenant armada" is given as the reason why Red and Blue Armies are now fighting each other, because they have nobody else to fight. The Halo games are never referenced directly again, although the latest couple of seasons have started to pull the series back around to fitting into Halo continuity with mentions of the UNSC, Insurrectionists, and explanations of AI that fit with the Halo explanations.
They go so far as to have the war between the Reds and the Blues be black ops meant to train their brand of supersoldiers (the Freelancers) against the Covenant, though the operation was a dismal failure.
The first three seasons of Arby 'n' the Chief were rather contrasting to later ones. The show was generally more situational as opposed to the overarcing plots of Seasons 5-7. It originally had a much more comedic tone with little to no serious moments. Plotlines often revolved around different controversies going on in the gaming industry (such as the claims that Resident Evil 5 was racist, panic over a glitch in Halo, and the introduction of avatars on Xbox Live)
Toy characters could originally interact with humans with no consequence. In the second episode when Arbiter is delivered, Chief signs a slip for the package and hands it to the mailman. Later on, this was strictly forbidden and Arbiter panics when Chief orders pizza and almost reveals the living toys to the delivery man.
Early episodes tried things that simply weren't well-received by the viewers or didn't fit in the series. New toy characters were introduced in season 2 that quickly disappeared. There was apparently supposed to be a storyline involving their disappearance, but this was abandoned in season 3 and creates something of a plot hole that was lampshaded in a scene at the end of that season.
A lot of the weirdness stems from when the early seasons were made. Chief used 1337speak much more gratuitously, and there were lots of references to now-dated internet memes or jokes that were already getting stale by the time the videos came out, such as Rick Rolling and a character representing anonymous and 4chan in general. Basically, you can tell that the early seasons were made in 2007-2009.
Even more evident if you watch the original "Master Chief Sucks at Halo" trilogy. The subtitles are at the top of the screen rather than the bottom, and they're white rather than green, as well as a different font. Chief already knows "The Arbiter", who speaks in the same manner as him despite the "current" Arbiter not showing up til the actual series. Fans have speculated that this is a different character altogether. Additionally, Chief himself speaks much slower due to Jon not speeding up Microsoft Sam.
In both Master Chief Sucks at Halo and early Arby n the Chief, the entire soundtrack is composed of music from other media. In particular, "Frolic", the theme from Curb Your Enthusiasm, is prominently featured to the point that it was considered the show's main theme. There was other recurring music, but after YouTube started cracking down on copyrighted material, Jon received some claims on the music and later seasons had their own original music.
Video quality in general was much fuzzier and very low-res. Scenes involving gameplay were even sometimes recorded with a camera rather than a capture card. This was partially due to YouTube lacking support for higher-quality video back then.
Series creator Jon Graham has stated that it also has to do with how troublesome it was to produce the videos. He often compressed them into 240p or 360p because they took far longer to render and upload otherwise.