Since getting my Nexus 4 and now Nexus 5, Nexus all the way.
I buy 2 flagships per year but I have an issue lol went thru 5 this year
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I think price plus the specs that you get for that price is key with the Nexus 4 and 5. Flagship phones will always have features not available or expanded on from AOSP. Manufactures want to make their product stand out from the pack with the latest and greatest, even if that means features that you can only get with certain devices or OEM's.I'd go with the new flagship every two. Being the first phone to get updates has never been an issue for me since I root and Rom my phones soon as I get them, and more importantly I've never been that impressed with the Nexus phones overall.
Of course the price on the new N5 is VERY appealing.
tap'n