I detest having the same protagonist for multiple games. Shepard went from being Space Marine Everyman to Space Jesus. It was dreadful. That, and it made the galaxy feel about the size of a single suburb. Shepard ran into people he knew in a hundred thousand light year radius than I do within 3 miles of where I live.
I think the way they handled Shepard was not a really great representation of how a trilogy with only one protagonist could work. The way in which Bioware was trying to make your save imports interesting was by having everyone you ever met come back to you. In a universe the size of that of Mass Effect, this makes no sense at all and was therefore in hindsight not the best choice ever.
I believe however, that it can be very interesting to have one protagonist throughout a trilogy or whatever, as I've always felt it to be really interesting to see how a character develops when facing new and different situations. I liked the fact that Shepard went from being a small time marine to one of the biggest heroes of the galaxy, just because of the fact that he was now dealing with entirely different outlooks and outcomes.
When looking at the way DA2 was handled for example, it seems as though it still has that bit in it.
There are three different stories, I really didn't feel they tied into one another that well to be honest, in which there's one protagonist. This protagonist has also risen up from Fereldan refugee (lowlife) to a hero and one of the most important figures in the city, whilst managing to still be a lackey for pretty much anyone capable of writing letters. So I'd rather have had a trilogy which fully managed to elaborate every aspect of the story and its background than to have it all stuffed into one game and have the game and story lose its value greatly.
I don't think Hawke's story would've been interesting enough for me to stick around for three games however.. 