I wasn't able to steal the ring for Brynjolf's first job. It was right there in front of everybody and I was fresh off the boat and wasn't playing a stealth race (I picked Dunmer, because why not?). In fact, I couldn't even get through the ratway, I had to polish my skills doing "freelance" work until my guy was good enough to reach them.
The problem with the guilds in Morrowind was there were so many quests, and a lot of them were so mundane. I don't remember ever fully completing any of the faction quest lines in Morrowind. I vaguely remember the Camonna Tong thing in Morrowind's fighters guild quest, but not really. They all felt like they were going to go on forever and ever, and it was just a slog, especially since my style of playing back when I first got Morrowind (Play a few hours, get an idea for a cool new character, play a few hours on him, get a different idea, etc.) basically ruined the beginning of the game for me. Like I said in an earlier post, the first ten hours or so of Morrowind were tread so flat it was almost more than I could bear to drag myself through them.
Also, I noticed Skyrim still hasn't figured out how to make rain respect overhangs. In Morrowind and Oblivion seeing it rain when I was under cover bugged me. Now it's kind of endearing, a quirk of the series that will never go away. Tamriel is a magical land where dragons are real and water is made of neutrinos.
As to your last point, the modders will likely have that figured out within the next 6 months.
As to quest line structure. My main problem with it in Skyrim, is that well, it's kind of too epic, too soon. The only line I've done to completion is the Companions, which I've been told strikes a balance between the way too epic of the Mages guild, and the Epic of the Thieves Guild.
It still has this utterly incomprehensable habit of removing player choices.
Allow me to give you an example, in the great houses, in Morrowind, you are given a choice, once you reach the requisite rank, of, do you want to be part of the governing council of the house, or do you want to lead that council. And the leadership role lead to about 3 more quests, as you killed or coerced people into joining your side. This is an example of giving the player choices, that oblivion and skyrim lack.
In terms of the quest structure. It lacks the buffer that Morrowind and even Oblivion had that enabled the shock of each twist to set in. In the Mages guild in Morrowind, the guild master is a spy and a general no nothing twart, and no that doesn't need spoiler tags the games been out for 10 fucking years. You find this out, and then you are sent to, rather than confront the fool like an idiot, gather support. It enabled you to feel a connection, to the plot, to the general world, and to the game.
Lemme give you an example of a similar moment in the companions questline. "Hey, we're asking you to become a werewolf in secret. We like your style and are going against our de jure leader, to bring you into the fold. Accept or deny, we'll not think any less of you." "deny" "OK we'll wait." and now(caps are for emphasis, not for yelling) YOU CANNOT PROCEED ON THE QUEST LINE. YOU CANNOT TAKE ANY RADIANT QUESTS. FINALLY YOU CANNOT TELL THE DE JURE LEADER ABOUT THESE PEOPLE. UNTIL YOU BECOME A WEREWOLF. BECAUSE CHUH, WEREWOLVES ARE COOL.
Here's an option, let me do radiant quests, and do the quest to get a head for the de jure leader, but each time I come back into town from each radiant quest, have these two werewolves attempt to drive me into a rage, badger me with conversations and requests for random shit, like 30 forks. Don't let me do the retribution and fighting the silver hand quests until I become a werewolf. Also basically haze the shit out of me until I go werewolf. Hell you don't even have to be that obvious. Have quests trickle out incredibly slowly. Until I become a werewolf. Have them inform me that they are basically using their influence to shut down my progress in the companions, until I become a werewolf. Have them have people send me on illegal missions that basically give me bounties in the other cities, until I become a werewolf. Give me options beyond a binary, gain a shitty power, continue on quests. Or don't gain a shitty power and be stalled completely in a questline.
That's without pointing out the logic of, this person has done at most 4 missions for the companions before becoming a werewolf and joining the circle. What about epic Australian dark elf(Only reason I legitimately purchased this game, heard him off in the corner during a lets play, and had to find out what he was.)? When's he gonna get the secret decoder ring. He's been here longer than I have, probably shown more dedication that this cultured and refined not fur wearing* female Breton ever has. What about the man that Vignar saved from the drink? What about Vignar is he circle? That's never elaborated upon.
*Coincidentally I did eventually start wearing fur after completing the questline, but that's because Saviors hide is good for when I face off with mages. I have a suit of equipment that gives me 100% magic resistance when combined with the bretons natural resists(25% from race, 20% from ring, 20% from amulet, 15% from armor, 20% from shield). Which somehow still translates into getting one shotted on master difficulty by every mage. Despite being supposedly immune to magic at that point. At least I'd assume that's what 100% magic resistance means.