Actually if you look at sales figures then the D3000 is the best selling Nikon DSLR by far. A D5000X would mean the same camera with a larger sensor. That might happen but not before a D90 replacement. If you want to know what the next D90 will have over the current D90 then look at what has happened in the past.
The D70 started it all back in 2004. The D70S came in 2005 with a bigger LCD screen and better AF performance and a few minor updates like a wired remote connection instead of an infrared receiver.
The D80 came out in 2006 and had a bigger LCD, viewfinder, and more megapixels. It had slightly better ISO performance and 11 AF points versus 5 on the D70/S.
The D90 came out in 2008 and it had a bigger LCD, viewfinder, and more megapixels. Nikon switched to a CMOS sensor where the previous generations had all used a CCD for much improved ISO performance. And of course it was the first DSLR in the world with HD video. It still had the same 11 AF points as the D80.
So for the D90 replacement (D95?, D7000? or D9000?) I think it's a safe bet to assume it will have more megapixels (either 14mp or 16mp - based on Sony sensors), better and faster auto focus since the AF module is very old design (perhaps as high as 39 AF points?), a bigger LCD that swivels, and much better HD video. I think ISO will be slightly better but probably be the same range as the current D90.
The D300S replacement will be out a "few months" later and will offer even better and faster AF, better ISO performance, bigger viewfinder, more external controls and a much more robust metal body.
Unless Nikon brings out an affordable full frame. In which case all bets are off!