In New Vegas, when in Mr. House's bunker, what is the best choice to make, when thinking of future gaming? Destroying the bunker, or helping Mr. House?
Essentially, there are four 'endgame' paths. You can align yourself with Mr. House, The Legion, The NCR, or 'None of the Above' (the so called 'Wild Card' option). Of the four paths, two will directly benefit from doing as Mr. House asks and upgrading the Securitrons - Houses path, and 'None of the Above'.
In the end, Fallout is a role-playing game, with the emphasis firmly on that phrase. Do what makes sense for your character for the story you want to see unfold. The multiple outcomes available means that if you want to see it all, you'll be doing another play through at some point regardless. There is no 'best' outcome from this decision.