Where to begin... well I went through your entire post and here are some of my thoughts/comments.
Part 1: Unfortunately, there is only so much that can be done in an MMO setting where story is concerned. Killing mobs are a part of the mainstream MMO experience and while stories with longer or more involved steps may be appealing, there is a framework that is hard to stray from without taking certain risk. I think there are a healthy number of companion quests but I would welcome more. When it comes to story I would like to see legacy related quests, where the character you play meets other characters in your legacy.
Part 2: Legacy Names (or family names) are no longer unique. You should have no problem having the same Legacy name for all the accounts in your household. That is assuming you have a legacy rename option available or have yet to create the legacies. Your legacy characters can be unrelated by hiding the legacy name. The way I understand it, legacy names can be family names though they are not necessarily family names, if that makes sense to you. They are only considered a surname if you choose them to be, legacy title or surname. You can show your legacy when you start a new character, assuming you have already created the legacy. I think there is a reason it is called Legacy instead of Family system, because it is not the same as real life, thus your comparisons are somewhat unnecessary. I have no comment on canon names.
Part 3: I'm sorry but I don't know what you are talking about here. There are themes for each world, music is triggered in combat, cutscenes, flashpoints, etc. What do your percentages mean? They have already improved travel significantly from launch, and added the quick travels for the daily areas. I don't see how the pace of leveing is slow in any shape or form, there are xp boosts, quick travel reduction times through legacy unlocks, the rocket boosts can now be purchased, etc. The entire color system could be improved for gear as can the crafting system. The whole idea of lightside darkside options for non-force users show that it doesn't matter if your character is jedi/sith or not. Apparently the force surrounds everything, I don't know, take your pick. Datacrons are optional, while they can give you a boost at end-game they are meant to be a challenge to get, at least this is my view.
Part 4: I don't know what you're trying to say here exactly. Triggers are necessary because the idea is you complete your class story as you complete your companion story arcs. You can still gain max affection with companions regardless of where you are in your class story. Nobody said you have to buy companion gifts either.
Part 5: I think there are already enough sub-forums and categories to post in. Too many sub-forums seperate the community. Also they are only as effective as how people use them. Notice many people will simply post in General when a lot of the topics posted there could fit in one or more of the sub-forums.
Part 6: Sorry, I'm against your guild charter toolbox idea. Sure you could have people fill out these forms and answer general questions about the guild, and let people find a guild that matches their criteria on the list, but they will only know what the guild is really like once they join them. In the end, I would say it would be a waste of resources. The rating system would not work the way you wanted either, people would just get their friends or close allies to bump up their reputation, or worse give credits to those who give them high praise, it would simply be a popularity contest. What might work though, is to have an in-game leaderboard to display guilds that have cleared certain content, achievements etc. that way Guild X can't simply claim to be the best on the server without the hard numbers being open for public scrutiny. People could draw upon their own conclusions on guilds from these figures. Such leaderboard would also need a toggle option for guilds that don't want to be public or competitive.
Part 7: I would like to believe that end-game is an aspect of the game that keeps changing. There are tutorials for beginners, I'm not sure what you're getting at. Video guides seem like something more suitable coming from actual players and groups. I would rather see a guild run of an operation then a generic video from SWTOR with 'tips' on how to clear it.
Part 8: Tab targetting works fine for me, I'm not sure I follow your stone analogy. If tab target doesn't respond the way you want, it could be the way in which you position your character, that said, tab targetting has it's uses but is not the only way to target things.
Part 9: You have a gripe against grinding, that much is clear, but some people find it tolerable, even fun. If the model is broken as you suggest, then why do many players play these MMOs that utilize the grind? There must be something right with the system. I'm not saying it is the best or even the ideal way MMOs should work, to have players grind for gear, but are there better alternatives? Nobody is saying you need to spend 80 hours a week playing. Just because the game offers dailies, weeklies, does not mean you are expected to do them all.
Part 10: Space Combat can be improved but I think for the time being it should be seen as a mini-game and nothing more. I know many people are concerned with the addition of grade 7 ship upgrades and their inclusion in the cartel market and I hope they address these concerns and make appropriate changes to the game.
Part 11: This is how the game was designed. Many people would prefer more open areas and player created content but changing the overall design would not be an easy task at this point. I do agree though that this game could really use some sandbox elements but whether they are willing to implement this or can achieve this are two separate barriers.
Part 12: What is a sacred cow? Character renames and server transfers are something I would like to see answered properly but things change where money is concerned. As we have already witnessed, things that are said in the past aren't always how they turn out.