Much as I like the show they have so many story threads it seems like more get diminished and forgotten. Malcom Merlin pops back alive with the secret father link but then poof he's gone. The city politician that's running for mayor who moonlights looking like scarecrow(don't know if that's who he's actually supposed to be) while working with Slade but he's disappeared too. Also they kinda wasted Summer Glau as a guest by having her just bat a few eyelashes and trade some barbs with Oliver. The writers could do a better job planning the story out and not leave so many dangling plotlines.
I agree that they have a ton of side stories going on, but my guess is that both Merlin and Summer Glau are build up for season 3. My best guess is that Glau is somehow tied in with the League of Assassins, which would also tie in with Merlin and will create the ongoing story for season 3. Remember we still haven't seen how Sarah becomes the Canary. We know she was trained by the league though.
As for Brother Blood, I was also wondering if Slade killed him off screen or not because he hasn't been on the show for a while. Also this is what Wikipedia has to say about the comic book version of Brother Blood
The first Brother Blood encountered by the Titans was the eighth to bear the title. Seven hundred years earlier, a priest in the fictional nation of Zandia named Brother Sebastian killed another priest to gain possession of what he believed to be Christ's prayer shawl. The shawl gave him invulnerability and reduced his aging, but the priest he killed cursed him to be slain by his son before his hundredth birthday. Upon doing so, his son became the second Brother Blood. He, in turn was killed by his son, and this continued for seven centuries