Assuming you aren't independently wealthy, one of the important things to research is maintenance and repair cost. I did not do this before buying my used ('06) GS, and am now combing the internet trying to reassure myself that I will not end up buying the bike a second time from the repair shop.
On the one hand, there is the routine maintenance. The days when you could, for instance, set valve clearances with a couple wrenches and a feeler gauge. The Boxer has something of an inherent advantage since the working parts of the engine stick out to the side and are relatively accessible compared with a vertical triple. This should reduce labor required to perform routine service. I say "should" because I haven't checked.
On the other hand, there is repair. I don't know how Triumph puts things together, but BMW has a penchant for packaging up a lot of parts into expensive assemblies that are serviced by replacement. The classic examples are the drive shaft (over $1000 plus labor if a U-joint fails) and final drive (over $2000 plus labor if a bearing lets go). These things don't appear to fail often (odds seem fairly good you'll never have one break), but if they go it's big money.
Obviously maintenance and repair cost is not the only thing you should consider; if you fall passionately in love with one bike or the other you know you're going to pay for it. But it's good to go into these things with eyes wide open.