To replace Alfred, I use Synapse[1]. It doesn't have as many features as Alfred, but it does allow for shell commands to be run from it.
iTerm2 is the gold standard when it comes to terminal emulators. TBH, no console really comes close to it. In my experience, the only one that is even comparable is Konsole, which is for KDE. Installing it on a non KDE DE requires a lot of other KDE packages and looks like garbage in it, so I wouldn't recommend do that. I find that Terminator[2] is perfect for my needs when paired with Tmux.
[0] https://manjaro.github.io/ [1] https://launchpad.net/synapse-project [2] http://gnometerminator.blogspot.com/p/introduction.html