It seems like being at the mercy of the game titans is an unavoidable evil in this particular industry. Getting even one of the 'Big 3' (Sony et al) upset at you could seriously ruin your coverage- but what are you going to do about it? If the industry were full of tiny companies (relative to the size of the industry), you'd have the reasonable ability to resist the temptation of outside influence, but that's not the case here.
However, it also seems that NWR is too small and 'under the radar' for the big companies to care all that much about negative reviews. The site is staffed by highly dedicated volunteers and is not exactly a moneymaking enterprise in the same vein as Gamespot or any of the larger VG sites. And I think that's a really good thing. Nintendo or any other company really has no incentive to cow the site to artificially boost ratings or rankings, and we get high-quality, pretty well unbiased coverage.
This brings me to the third point. Baten Kaitos was a pretty craptacular game, looking back. I thought the sequel (Origins) was much, much better in most respects, which makes it 'on-the-par' for an average JRPG (although most people probably thought it was crappy as well). But Baten Kaitos was a low-profile game that wasn't heavily advertised and wasn't really expected to sell very well- which leads one to ask: were the impressions changed at the behest of a publisher, or were they changed to conform to an industry convention (positive impressions)? If it's the former, there really might be something to worry about.