There are four different parameters are play here: launch rod diameter, launch pad sturdiness, controller voltage, and controller wire length.
1) *Roughly*, rockets flying on 13mm or 18mm motors (1/2A through C, at least with Estes motors) will use a 1/8" rod. Rockets using D or E motors will usually use a 3/16" rod. 29mm rockets can use a 1/4" rod, but nowadays will more often use a rail.
2) Larger, heavier rockets require sturdier pads.
3) According to NAR safety codes, anything up through D motors requires launching from 15' away. E and F motors require 30'.
4) Single Estes BP motors (regardless of size) can start successfully with 6 volts, but more voltage usually works better. Clubs generally use 12V systems.
So: the regular Portapad comes with a 1/8" rod, and is fairly small and light. The regular Electron Beam controller uses 4 AA batteries to get 6 volts, and has a 15' cable. So the whole setup is geared towards smaller stuff, up to D motors if you use a 3/16" rod (sold separately).
As far as I can tell, the E launch controller is exactly the same (4xAA) except it has a 30' cable, so it's good for E and F motors. I would generally not recommend it, though; the Estes PS/II controller is much more robust and still quite reasonably priced.
The E launch pad, which I've not seen in person, comes with a 1/4" rod, which suggests it's really intended for PS/II rockets, which fly on 29mm E and F motors. I don't know how sturdy it is, and I don't know if it's straightforward to fit a 3/16" rod or a 1/8" rod, in case you want to use the same pad for all different size rockets.
So ultimately it depends on what size rockets you want to launch, on what motors. I generally recommend the PS/II controller regardless, because it's nice and can supply considerably more juice to launch more reliably.