It all started to go wrong back in the '90s, with Dark Empire. Heir to the Empire kicked off the 'modern' EU (post-Marvel, post-Han/Lando books), and then Dark Empire began. "Heir" showed us that 5 years after the films, the Republic was still building up, the Empire was all but defeated until Thrawn swooped in, and there you go. "DE" then told us that A YEAR AFTER the Thrawn Trilogy we'd just started reading, Coruscant was back in the hands of the Empire, the Republic was destroyed and back to being a Rebellion, and everything went to crap. So, tho Thrawn ultimately failed, the Republic still lost, due to the Emperor having a bunch of clones AND having a gigantic starfleet amassing around Byss that nobody else knew about (not even Thrawn!).
For awhile, I just ignored DE. I loved the art, I liked some of the covers, I even enjoyed the concept (until DE2 and Empire's End came along). But it didn't fit with the story I was thoroughly enjoying over in the books. But when the Jedi Academy Trilogy came along, I realized the comics and books WERE meant to be connected. I also realized that KJA was like an internet fanboy given leave to publish his fanfic. "Ooo! I'ma make a superweapon that doesn't just destroy a planet, but destroys a STAR! AAAAAAND I'ma put another Death Star in there, too! And a kid who's even more powerful than Luke! And a Jedi Testing Contraption! And a 6-foot-long saber blade! And revisit Bespin, cuz why not?" To be fair, I loved the idea of a Jedi Academy, and setting it on Yavin IV at the old Rebel base. But so much else in that trilogy came off as rabid fanboy let loose in George's toybox.
My biggest problem, however, with Bantam's era of the EU is the patchwork nature. Here a trilogy, there a oneshot... and they didn't progress in an orderly fashion. We start several years after the film, then get a book starting the day after Return of the Jedi, and then Bantam just jumps around the timeline, finding and gap where the OT heroes could be resting on their laurels and throwing another galactic crisis at them. Authors had their babies like Mara Jade who were often misused in other authors' books (hence Zahn's retcon of why Mara & Lando appeared to be an item at one point). There was no set plan, just "tell a Star Wars story, don't reference the Clone Wars too much, don't have Luke find out anything major about the old Jedi Order or his mother, and maybe have Leia train as a Jedi a bit." It seems like Leia became a Jedi Knight 8 times during the Bantam era, only to be 'reset' down to 'politician with a bit of Force training' in the next chronological book. They didn't need a gigantic storyarc like Del Rey's 3 big tales, but some steady progression would've been nice, with better oversight on how the characters were used (so Mara & Luke wouldn't have to wait 10 years to suddenly realize they were perfect for each other, Leia wouldn't constantly put off her training only to become Super Jedi for a week, then back to being just a politician, etc)