I agree with your season 1 assessment that Astrid was underused but Charlie I think was natural that he would be only a supporting character.
I differ a bit on season 3 because I think they've done that really well and it's hard for me to say that because, as I said on a different Fringe thread, I really struggle with situations where we know big things that the main chars aren't aware of. As a result the whole shapeshifter Charlie (same concept) and especially the Altivia over here thing deeply irritated me but yet they did it so well I couldn't find a way to fault it.
Now we have everything back in place and so much potential for the show to go forward. I know what you mean about the observers, the sort of chars that will always appeal to me but to be honest they have done well to underplay them. If you focus too much on a powerful / exciting 'race' like that then they would tend to take over the narrative and the show is about the Fringe team not the observers.
The weapon will build in more, I think that's part of the big arc of the series. Aliens,well I don't think they're ever going to really be a part of this. And Rachel / Ella I don't have a problem with how they've been handled. Really they were just a way to humanise Olivia and to play off the Peter-Olivia sexual tension (at least as I saw it) so I can see that in a way they're no longer needed, at least for now.
All in all a top show and it seems that for whatever troubles you have about the series there's clearly enough interesting you to make you another Fringe fan with the rest of us