The fact that there will be PvP disturbs me, I've yet to see an MMO were the PvE side wasn't negatively influenced by changes meant for the PvP side of the game.
The new level up system kind of irks me too. The fact that they aren't adding some of the guild types isn't good, and no, adding them later doesn't make it better. MMO history suggests heavily that the first impression is the only one that matters, MMOs that have fixed the majority of their release problems/lacks have shown that doing so doesn't typically get people to give them a second chance after the first taste is found wanting.
Their response to the modding question was expected, but at the end of the day it highlights the most glaring thing wrong with TESO. That it's not the single player, Elder Scrolls experience the fans expect or want. There are very particular sets of reasons people keep coming back to the TES games, and the modding community, like it yourself, or not, is one of them. No matter the excuses the developers, or the fans, will make this 'will' hurt the game. No, it won't kill them game. It will just hurt it. Yes, oddly enough when something you've come to expect from a series is suddenly gone, some people get turned off, and you lose a sale. Whodathunkit.
Obviously, this does not only apply to mods, by way of this being a multiplayer game, and not a singleplayer game, there are more than a few features of TES we know and love that are simply not going to be present. This highlights one of the most obvious problems with a TES MMO . . . 'if you're not making it in the style appreciated by your current, established and very large, fanbase, then who exactly are you making the game for?' For all the things you might bring up present, there are still a large number, well documented, that are not going to be there - these are things this developer has outright said won't be there. To the extent the developer outright told in the first place that TES fans may not like this game. Which is an insane thing to say, "We're making a TES game that fans of TES are probably going to hate" is one of the most mind boggling mission statements I've ever heard.
I think the only thing that could really kill this game, though, is if they tried to release it as a pay to play MMO. Monthly fee MMOs, outside of the very rare, particular and older MMOs with an already present loyal fanbase have largely gone the way of the dodo. The ones that still remain, are the exceptions - and yes, WoW is a major exception, literally nothing else is like it in the industry, and MMOs like Rift are also an exception (but for different reasons).
The thought that 'my MMO will be different, it will be an exception too!' borders on ridiculous, the delusions of an unstable mind. I'm very sure that if TESO is released as a pay to play MMO it will go down in flames, or turn to a buy to play or free to play model. From the recent industry successes . . . it would seem free-to-play (no monthly fees and no purchase of the game with cash shop) or buy-to-play (buy the game at full price, play forever with no monthly fee - with cash shop, and occasional expansions you can choose to purchase or not) are the current models that actually work, and actually get people to play your game.