Another viewpoint:
I find that the D40 with it's easily read menu options is far easier for me to operate than a camera with a lot of tiny buttons... (I had a D70, and disliked it because of that!) If you have older or ~weaker~ eyesight, all those tiny so-called 'direct' buttons can be a real hinderance because they're pretty much unreadable and have to be memorized...
(And then if you also have a ~weaker~ memory?? ">})
There's also a function button on the D40 you can dedicate to anything you want, and I use it for ISO changes. But also so far I've not found using the D40's menus to make any other changes anywhere near what I would consider a "long time". I mean, I'm not a war photographer who needs a combat-fast DSLR, -as really most of us aren't?
And stick to the scene modes? Well, I may not use the strictly manual option very much (and do most D90 users do this?), but I'm always using the S or A priority settings, or sometimes the variable P settings, just like I think most Nikon DSLR users do... Also the D40 shoots great hand-held shots at such low speeds as 1/15 and 1/30 sec because of it's extremely low shutter and mirror vibrations. Does the D90 match that? (It may, I don't know, I'm only asking here?)
And IMO the hype about MORE megapixels is mostly just that... Unless you're shooting for huge prints, in many cases 6MPs are actually better than 10 or 13! For example the D40 with 6MPs is actually rated better than the D40x and the D60 and D80 with their respectively greater MPs, as it gets a good rating for noise at ISO 800 and an acceptable one for ISO 1600 while those other three 10MP cameras only get an acceptable rating for ISO 400-800 and an unacceptable one for 1600!
If I were to ask Uncle questions about which camera he might prefer after indeed checking out which lenses he already has (a very good question!), if he didn't have a lot of older glass (which would definitely then make a D90 or a D300 better), I would then ask whether he preferred a heavier, bulkier, more complicated camera with excellent low light capability but with rather average video options (the D90, D300), or would he like a highly efficient, fast, easier to operate, smaller DSLR with no video or excessive options, that also has excellent low light capability, and is a DSLR that takes fantastic shots with a variety of good AF-S lenses and a minimum of fussing about?
Of course YMMV as to what you prefer... But IMO, with Nikon (and many other DSLRs) the number of MPs and the cost of the camera are sometimes just hype designed to get folks to spend more, and as such these parameters can become mostly irrelevant when it comes to judging the quality of a DSLR...