Well, technically Shogun and MTW were already 3D games, except for the campaign map and the soldier graphics.
You are however somewhat right but I do not think the blame lies on the 3D graphics themselves but rather on the added attraction they give to games which attracts more casual players the companies then try to cater to.
3D graphics offer some great possibilities as well, if the developers use them, but in many cases they just try to make everything easier so the game almost plays itself, one could say they make games more like TV shows because that is what people are used to, but if you think about it they could do the same with 2D graphics so I think the connection to 3D is coincidental and there are some pretty good 3D games out there as well.
Personally I liked M2TW quite a bit, sure it wasn't perfect but I had a lot of fun with it, then there is the Thief series which started out in 3D and many here like a lot(personally, as usual, I just played the demos ).
And I would like to add Gothic 1 and 2 which also never had 2D versions and are pretty excellent if you don't start crying about the controls for reasons I never understood, the third part however was pretty botched and incidentally was also the first part the publisher wanted to make big in the USA...go figure...

And then you have quite a few games from the russian-sphere or Eastern Europe/Russia like Operation Flashpoint, Armed Assault(though with StarForce afaik), the Stalker games etc. IMO no matter what graphics they use, the eastern games companies usually make pretty cool games they release in a pretty buggy state, usually they draw me in for weeks even though there are bugs and problems, quite different from all the accessibility and streamlining that turn many western games into a bunch of quick action scenes between a bunch of cut scenes.

But generally my point is that the 3D graphics are not to blame, they just made gaming more popular which made many companies change direction towards less depth, something I find fun as well now and then but not in every game and genre.
whether less depth was actually demanded by the masses or just assumed by the publishers I find hard to answer and could end in endless discussions.