Flybe -V- BA. The age old question.
My first point: - are you seriously only looking at two companies??? I applied to everyone I could, within reason. One person I know has ended up with Cathay Pacific after years as a flight instructor in Florida waiting for an airline slot. Aiming at just one of two airlines is, sadly, unrealistic and short-sighted. We all have our dream slot, it's true, but you must open up your horizon.
Pay is an important factor, as are conditions. FlyBE also have jets, and it is often heard how the management there want to go pure Embraer. You may want to dig a little deeper in your research.
Turboprops may be more interesting to some than to others. The Q400 is certainly a powerful machine. BA fly transatlantic with the A318 though as well so you can be statesside operating a mid-range jet and still be operating from London City.
My personal choice in an ideal world though would he BA. Larger, more secure company with a very strong market position, more varied routes, the glam of being the "flag carrier" (although Virgin Atlantic love to dispute that one), to name but a couple.
Good luck with your training and career and I hope your first aviation job is something close to what you want.