There weren't many intentional changes. (Not counting ENT though, that's when the continuity started to fall apart.)
Oh yeah? Are the Klingons Fu Manchu-looking anti-Asian racist stereotypes like in TOS, bald guys with a single thin ridge down the top and front of their heads like in TOS, or bumpy-headed dudes with long long, curly hair like in TNG?
Are Trills a Human-looking species with spots whose humanoids join with symbionts to create a new person with each joining like in DS9, or are their human hosts just mindless shells with bumpy foreheads and noses whose real personality is housed in the symbiont?
Does the
Enterprise-A have 20-odd decks, or 80-odd decks like in TFF?
Did the Klingons join the Federation like in early TNG, or were they always a foreign power like in later TNG?
How many fingers do Tellarites have?
Did the Romulan Star Empire have warp drive before the 2200s, like the admiral in INS says they didn't?
Was Vulcan conquered like McCoy said in "The Conscience of the King," or is the idea utterly foreign to Vulcans like Spock says in "The Immunity Syndrome?"
Does anti-matter power warp drive like in most Trek, or does it destroy the universe like in "The Alternate Factor?"
Does Data have the ability to use contractions and feel emotions, like he does in early TNG, or is he emotionless and incapable of using contractions like in Season Three onwards? Did his emotion chip, which was established to be fused into his system in GEN, just disappear by NEM?
Is Miles O'Brien an enlisted man like in DS9, or an officer like in TNG?
Do they not use money like in TVH, or does the Federation so rely on money that their dilithium miners can get rich like in "The Devil in the Dark" and there's a black market for human trafficking like in "Mudd's Women?"
How the fuck many Rigels
are there, anyway?
Does Vulcan have no moon like in "The Man Trap," or does it have a giant moon like in TMP?
How many goddamn shuttlecraft did
Voyager have when it was launched?
How come the Federation had transwarp in TSFS but it was an elusive technology in VOY?
How the hell big was that HMS
Bounty bird-of-prey Kirk stole anyway?
How can the center of the galaxy be like three-days' journey in TFF but it takes 75 years to get across the galaxy in VOY?
Did Praxis explode three months before Kirk's trial in TUC, or was it only a few days later like in VOY's "Flashback?" Did Valtane die like in "Flashback," or was he alive when the
Excelsior left Khitomer like in TUC?
Is Klingon blood red like in most of Trek, or purple like in TUC?
Why was Worf back in a Starfleet uniform serving aboard the
Enterprise-E in NEM, when DS9 ended with him becoming Ambassador of the United Federation of Planets to the Klingon Empire? Why was
Wesley back in Starfleet after renouncing it to become a god in "Journey's End?"
Was young Picard bald as a cadet like in NEM, or did Ensign Picard just out of the Academy have a full head of hair like in "Tapestry?"
Did Beverly go to the Academy like she implies in NEM, or was she
literally an infant during his time in the Academy as TNG established?
Why didn't Soong mention B-4 in "Brothers?"
Was Spot a male or female cat?
Did Kirk's
Enterprise have a spike coming out of the bussard collectors or not? Did it have round bumps at the back of the nacelles or not?
Did the
Enterprise-D have a thin edge along its saucer section like in TNG Seasons One and Two, or a thick one like in TNG Seasons Three through Seven?