1. In the books, the mystery was infuriatingly hard to unravel, and never fully resolved, but here it's straightforward: the children's parents belonged to a secret society dedicated to "putting out fires." A number of years ago, a group led by Count Olaf split off and dedicated themselves to "starting fires" instead. The children are caught up in a war between the two factions.
2. The settings and costumes are beautifully realized, Depression-Era in The Austere Academy, Jazz Age art deco in The Ersatz Elevator, 1950s Cold War in The Hostile Hospital, with only a few of the books' anachronistic references to streaming videos and the internet.
3. There is a lot more humor in the series. In the books, it was unrelentingly depressing, with any humor coming from wordplay.
Of course, there are flaws:
2. The hetero-romance between the Baudelaires and the Quagmires is only hinted at in the books, but in the series, it takes center stage. Even when they're searching for their kidnapped friends, Violet yells "Duncan!" and Klaus yells "Isadora," as if the same-sex Quagmire doesn't even exist. Have to emphasize that these kids are heterosexual! Don't want any of those pesky gay subtexts!
3. The action drags and drags and drags. A very short book adapted into two 45-minute episodes means a lot of reaction shots, irrelevant comedy bits, and even songs.
4. No gay characters, except a couple of the villains, by implication.
6. No beefcake. A lot of the actors are buffed -- even Louis Hynes (Klaus) somehow managed to develop a physique --but no one unbuttons a button not even Robbie Amell or Nathan Fillion.
7. This is kind of nitpicky, but, however evocative the name "Lemony Snicket" is, when you say it aloud, it sounds silly.