Zhxie, I'll just share my experience with you for whatever help it may be. I've shot Nikon SLRs since the early '70s and have accumulated a few lenses. One is pre-1977; most are AI or AI-S and one is AF, though, as of 2005, I was still shooting my FM-2n and FG (with a Nikormat FT-n for backup) and did not yet own an AF camera. In 2005 I decided to get a digital camera, studied and shopped hard, and got the D70. It surpassed all my expectations, except that I had no metering or AF with most of my lenses. Being somewhat old-school, I could always set exposure and focus fine manually. Then I got some more AF lenses and got spoiled. Even though I only use them about half of the time, I found that AF and auto-exposure were tools I didn't want to be without. The D70 is not the best at auto-focusing, and it had no metering at all with my AI lenses, so, after 18 months, I stepped up to a D300, which gives matrix metering with the AI lenses and AF with any AF lens. It was the best move I ever made and I enjoy using it so much that I followed up by buying a used F100 so I can also have all the modern conveniences while shooting film.
You aren't bogged down with older lenses like I was, but many excellent AF lenses are not yet available with AF-S or AF-I focusing (the last two lenses I bought were 85mm f/1.8 and 30mm f/2.8, both AF), so I would think hard before buying a camera that can't AF with them. Of the two cameras you mentioned, the D90 is much safer in this regard than the D5000 (though I think they're both excellent cameras), and you might even consider getting a used D200 or D300 to get further flexibility with lens selection.
Just my thoughts. Hope they help. In any case, good luck.
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