As Sue says, Ken Rockwell is (usually) an idiot.
If you've no experience with SLRs then you'd never notice the read/write times on ANY camera as they'll all be considerably faster than your compact.
In reality (again as Sue has said) all the entry level cameras are pretty similar. In my opinion the best all round value for money kits are from Sony & Olympus. You'll get a bigger range of accessories and options from Canon & Nikon but you'll pay a little bit more for it.
You seem to have done some decent homework and come to sensible decision. If you want a more in depth and much less biased review of the D3000 have a look
here but you'll not be disappointed with it.
Ignore the D40, it's too old, not worth enough and the technology has moved on a long way, especially in the AF and metering systems which are pretty important!
Ah, and the Guide mode on the D3000 is actually very good. It's well laid out and very easy to understand.
All in all you won't be disappointed with the D3000 and you'll have a
much better all round camera than the D40.