I don't get what the problem is.
Shephard is awesome character(At least mine is
) but having an influencial character has its limititations over the series.
For example: I'd hate to play a Darth Sidious game starting at level 1 for example. We're talking about Sidious here! Not some typical human. (Many developers including big boys like Bethesda, Obsidian and Bioware fell for that. "You are x! Too powerful, bringer of balance! Fate of y is in your hands! But stay away from dragons for a while heh... Didn't buy it? Thought so, still keep playing.")
So even i loved Shephard, especially female one, thanks to Jennifer Hale, it was time to move on. (One of main things i'll miss is Jennifer Hale as main VA btw -.-)
Some people didn't like ME 2 or 3, this and that choice's consequences, ending... Trilogy has some problems to some people so to speak. I love them all just to record.
I always thought ME(And DA too) as universes like Star Wars.
Of course both KOTOR and SW:Episode 3 belongs to same universe and has similarities but neither has a limitation over another. IIRC that's the main reason Bioware chose a timeline which was far away from movies, to have freedom.
Not mentioning the newcomers. Some folks may not even heard of previous games or didn't have PC that time or haven't even heard about it.(Living in a cave? Ehh) Some may not be at availible age when the first game came out. Some may hated the changes. Some may hated the original games but loved others.
Having choices in game is awesome, until developer decides yours is not canon.
I totally wanted to kill whole council with no replacements because councils are there only to postpone stuff until their next pay check(A council of Anderson, Garrus, Tali, Mordin, Legion would be ftw though... Until they get lazy too, because council=being lazy in every single game/book/movie), i never liked Udina but he got "promoted" even i chose not to because it was canon after some book.
So many options and these actually handicapped the series really.
So in next ME it is understandable that they're changing the "place", i hope they'll change timeline too. Anything that can limit Bioware or any developer results in bad games that only has a cult following it.
But it would be cool to see our Shephard by video recordings or if timeline is near to hear about him/her in news etc.
Bioware only need to make choices to have more consequences, more grey choices instead of white and black, represent paragon not as "white knight" while renegade not as "angry adolescent" and i'm pretty sure it can even pass originals.