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The only downside I see to House is that he's running casinos and such instead of building stuff or making medicine. I'm sure House could put the brotherhoods bunker and equipment to better use than they did.
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I don't like the Brotherhood of Steel and its fairly easy to wipe them all out with the right weapons so doing that part of Houses quest line doesn't bother me. If there is anyone in the Mojave I like (like the Kings, the Follower, Goodsprings or whatnot) then I just have to keep them in Houses good graces. House seems like a man with a plan and the brains, tech and resources to carry it out. House to me seems a lot like doing the Yes Man quest except he has a long term plan while I'm basically a one-man army (heck, even if Yes Man was deleted from the network I could take out House and have Emily code up another AI to run the system for me if the need should arise).
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Granted, having both the NCR and the Legion on both sides of his empire would make things difficult but I'm sure with adequate amounts of bribery he could get the NCR to do as he wants while using the Legion as a common enemy for whoever else he has to negotiate with. House since he wants a high-tech future, immortality (possibly which could benefit me as well), and he would be easy to usurp if the need arises.
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