For beginners I would say most of those are non-issues, Nikon know this and it's why they cut costs with those features, for the market they are aiming at they are for the most part not a big deal and certainly won't be debilitating to the average user. Whilst the D80 kit is silly cheap at the moment I would recommend that all day long, but usually the D40/60 is more than good enough.
For those spending a couple of hundred they aren't likely to want a £150+ Nikon grip, so the perfectly good 3rd party ones are more than sufficient (Hanhel in particular are very good), very few people are likely to want to use a lens old enough that it doesn't have CPU contacts, the software supplied is no better higher up (D90/300 doesn't come with anything special) and RAW + L JPEG is hardly a deal breaker, I'm guessing 90% use JPEG anyway. The only real issue is the AF motor, but Nikon and the third party manufacturers are moving most things over and in time that won't be a problem.
I had/have a D50 which has all of those 'faults' (apart from the AF motor) and it served me perfectly well for two years. I shot motorsport quite successfully with only 3 AF points, never caused me any issues, and there are 1000s of photographers shooting stunning stuff with D40s/60s.