Let's see....
Original BSG, despite the hopeless nature of the fleet's situation, was still optimistic, about humanity banding together for their common survival.
The remake everyone was pissed off at each other's throats the entire time. NO ONE was even the remotest bit likable.
The original Starbuck was a scoundrel and rogue, a lovable Han Solo-type. The new (female) Starbuck was just an insolent, insubordinate *****. The altercation between her and Col. Tigh at the beginning of the remake mini illustrates this perfectly. For that matter, why the HELL did they make Starbuck a woman anyway? I read the interviews, they wanted a character to have sexual tension with Apollo. Well they frelling DID. What happened to Carina and Sheba?
Hell, for what bloody purpose did they need to make Boomer a Cylon fembot?
Apollo was just a jerk in the remake. His attitude towards Adama in the remake was completely out of place and unbelievable.
The original Baltar was FAR more interesting. Self-serving, twisted and maniacal. And he got neutered and turned into a poor sap getting led around by the balls by the Terminatrix.
Then there's the plot itself...
Ok, yeah, so the computer virus was an interesting twist and illustrates the more cunning Cylons of the remake. But the fact that the Colonial military is SO integrated that there's no fail-safe should something happen on one ship thus crippling the ENTIRE fleet is ludicrous. Haven't these people ever heard of firewalls and anti-viruses? Even your typical, run-of-the-mill fully-integrated business network today isn't going to COMPLETELY go down just because of a virus shutting down the Domain Controller, because the individual workstations STILL have the capability to function totally autonomously, even if they can no longer access shared or networked resources. Is the entire Colonial fleet running dumb terminals? AND the fact that Adama was ALLOWED by the Colonial high command to refuse to upgrade the Galactica's computer systems to integrate them with the central defense system is BULLCHIT. The Galactica is NOT Adama's ship. If the fleet orders you in to dry dock to upgrade, you report to drydock to UPGRADE, or you get replaced by someone who will. Contrived, weak and totally unbelievable.
Oh, and then there's the weak incident where to throw suspicion off himself, Baltar fingers a random guy on the Galactica's bridge to be a Cylon imposter....only to discover at the end of the miniseries the guy actually IS a Cylon imposter (I won't get into the fact how FarScape handled the Harvey mind clone of the series villain WAY better).
Also, why with FTL flight capability does the entire Colonial military still use physical round-based weaponry?