You only need to worry about 'Nikon AF motor in body' if you plan to be an 'anorak', ie., part of which is collect old lenses, to some, its as much part of the hobby as taking pictures:shrug:
My limited experience indicates that the newer Nikon AF-S lenses focus faster, quieter, and I would hazard a guess, 'more accurately at the lower and entry level' end of the market . . . ?
Third party manufacturers are covering widely, the new Nikon AF-S system . . . Its taking the die-hards a bit of time to catch up . . .
As for the D5000, its streets ahead of the D3k. The 5000, is within a gnat's whisker, 'a D90 where it matters' . . . and you have the swivel screen as an extra.
You may feel the kit lenses are letting the side down . . . believe me, they will be as good as you for a long while, years, not months? By that time you will understand the hobby better, be able to make your own decisions on the direction you wish to take.
See here, make comparisons:
http://www.dpreview.com/reviews/nikond5000/
http://www.dpreview.com/reviews/nikond3000/
Especially read, 'Conclusions' and 'Final word', a less technical summing up.
CJS