While the basic Torchwood setup is fine, the main problem with it is how small it is compared to Doctor Who. Sure it was enough to run two years of it and two serials, and nine years of The X Files and four and counting of Fringe, but stuck in a single point in space and time, you need a decent reason for the PCs to face a new alien-related threat every week.
(Skywatch has "official sanction for events like this across the UK" and the Whoniverse's "this kind of thing happens three times a week". Torchwood adds the Rift, a spatiotemporal Hellmouth.)
They should generally be somewhat more low-key as well - alien incursions in ones and twos rather than hundreds and thousands. Torchwood Three work on a global scale at most. Even their Big Ten-Parter which changed the world dramatically for months could probably have been solved by the Doctor in a single episode.
So a lot of these will be ringing the changes on Aliens Of London. (Or Cardiff, or Glasgow, or MediaCity Salford...)
So to start with, there’s an alien on the loose, attacking and possibly killing people, for some nefarious or baffling purpose. It has to be stopped.
Ideally without (much) gunplay because chances are it’ll laugh off bullets like drizzle. The team might be able to combat it directly, but that will be tricky to set up and arrange, especially if they’re trying to keep quiet about things.
(If direct combat is likely to be a frequent thing, consider adopting the initiative system from Primeval which divides characters by speed rather than intent.)
Since this is the pilot, don't ring the changes too heavily. A single alien active near the team's base to some dangerous purpose, intentional or not.
Example: The Watcher In The Dark
A group of young people out camping see a shooting star, send a video message home - and disappear. Seven days later, one of them stumbles out onto the road and flags down a passing car, babbling about having been abducted by aliens. Tests at the hospital show that she has a slight case of the bends.
(And for added involvement, she's one of the PCs.)