Indeed...I don't think the ending was that bad...it's just that it wasn't complete...I liked the epic or fancy ending, and it somewhat played along with the theme of sacrifice...and it wasn't that unexpected either...in my ending Shepard dies, and I didn't even get the 3rd option and my romance was Liara...so while I always got hints of blue children and love, and surviving this and that, in the last arc, Liara and others have hinted that Shepard might not survive...
But as you said, it doesn't really reflect the character, or maybe it doesn't reflect the choices and the life with UR crew...so an Epilogue would've been nicer, or an ending where Shepard survives or convinces the Catalyst to do something else than the 3 choices...there's no closure
But the individual story arcs...my god...Mordin's death, Thane's death

, the fall of Thessia, the mystery of Cerberus always hanging over your head...I think the mass killing of ME2 really added to the drama...I have no words and had no words at some of the developments...Thane's death was the best...
Resources....I was waiting for a mission with Aria's mercenaries and never got it....that sort of left a hollow feeling...though I agree, and actually there is one thing that the resources influence...whether or not Anderson dies, and to what degree is Earth destroyed...I think that's about it though
The Prothean was nothing impressive...the only interesting thing he added to the story is that the Protheans were sort of enslaving others...but that's kinda it...I think Kasumi from ME2 was a better character, and definitely a more useful squad member. Stealth FTW
And I played as Paragon as well, though I messed up my last ME2 playthrough and Tali got killed, so I have no idea if there's an option of making the quarians and geths to make an alliance...but that will be my next playthrough...also I always play with a biotic and someone who has a nice special ability...so I used Liara and Ashley as much as I could...
/me doesn't like Garrus at all...