I actually liked the ending too, but mostly because it wasn't what I thought it would be. Yep, there are alot of filler episodes, but more than anything they serve as a way to link up different characters as majority of them are linked to one another in ways they don't know.
For example, Winry's parents were doctors at the time of the Ishbal insurgance, and they were killed. We don't know by whom at first but later we learn it was by the military (I wont spoil the surprise and say who) and it kind of changes your impression about characters. Thats what I like about this show. The line between the good guys and bad guys is often blurred. My favourite twist was when you learn why Envy is named Envy and just why she is jealouse of the Elrics. FMA really is a well constructed story.
I definately think you wouldn't be able to fit this series into 26 episodes, the story is too big for that. This is the first series that has kept me hooked for that long
As far as character sympathy goes... well, at first its a bit hard to feel emotion for a suit of armour, but the Elrics do go through alot but they don't feel sympathy for themselves. They now the consequences of their actions and try to deal with it. Towards the end, it's more about what the Elric brothers are willing to sacrifice to save each other and I believe thats the heart of the story.