Can you give an example of a particular one you thought was badly done?
Many of the major quests essentially put you on rails. One of the worse are the Markarth ones dealing with the Forsworn. In this chain, due to the nature of most of the inhabitants of Markarth, I didn't want to help them, I wanted to help the city by removing them from it; especially that corrupt arrogant Thonar (such a dick). Of course, Bethesda wouldn't allow that. No, I had to reload, and roll sadly along, being forced to "brawl" with Dryson, some lowly thug bent on "teaching me a lesson". I especially loved the part where I'm violating the law for defending myself, because why wouldn't I defend myself with the huge sword that I carry for that express purpose?! The icing on the cake was that Dryson was an IMMORTAL THUG, and thus I could not defeat him with either blade or magic. No, Dryson's kryptonite was fists apparently, causing me to wonder why he didn't put his near invulnerability to better use (like killing dragons you lazy prick).
Another little gem is the House of Horrors, where your offered no option but to slaughter the man you offered to help. Would it have been so hard to offer an opt-out clause, say, bash down the weak wooden door? Quests like this make Bethesda look lazy, squandering an opportunity to help the player create a narrative that suits the character they want to play. After all, when you take a quest to help a Vigil of Stendarr clear a house of evil, the last thing your thinking of is getting forced to commit it.
Are all the quests bad? No, and that is what makes it all the worse. Skyrim started out great, doing a good job encouraging players to feel invested in their character. But the built-up effects of all their hand-holding really ruined it for me. Handing-holding like Immortal npcs born of Bethesda's belief that players are too inept/lazy to protect an npc, and shouldn't be "punished" by failure (players can save/load anywhere, so the punishment is nothing beyond taking too much hp damage and dying). Handing-holding like Bethesda's insistence that all players should be able to do everything, resulting in overpowered characters who the game cannot properly challenge.
The quests that are good are the ones that do not force the player to run into Bethesda's awful obsession with hand-holding. The minute the player wants to kill an npc but can't, the minute a player is stuck with a bumbling npc sidekick that does nothing but block your LOS and break stealth, the minute I'm forced into some artificial "brawl" with some thug, and I can't blow him to bits, Bethesda ruins a significant bit of the believability of their world that they worked so hard to create through the millions they invested in their impressive visuals, fully voiced acted story, and large interactive world. Had they just applied a bit of that interactivity to their npcs, allowing them to die just as the main character can, then there would have been no awful quests in Skyrim.