Matt,
Its funny, but Medinah was always ranked top 10 or so until the '75 Open when JN criticized the old 13th (current 16)with its too short snap dogleg. After that, it dropped to the mid 40's or so, from memory. Yes, it has trees, but with some of the removals, is this course really much different than most US Open venues in its makeup? The current putting surfaces have been softened, but the old ones were quite nasty and fast by nearly any standard. That said, these probably fit the green speeds better for tournament and every day play.
As I mentioned earlier, the project this year lengthens the distance to the dogleg by putting the tee where the old 15th was, and I think they may have taken down a few trees, but the new placement also reduces the dogleg naturally. In reality, I think that was the crux of the project, and the driveable par 4 15th was simply a by product.
I pulled out Tim Cronin's "Spirit of Medinah" when thinking about the changes. While granting the course now looks more like Rees than a traditional course, I can't say the changes - like angling the green on 2 and most others don't "make sense" from a playability standpoint.
As to the routing changes, over the years, Roger Packard and Rees have bascially taken out the worst holes -
Packard removed the old 14 and 15, a mundane par 3 and par 4 and replaced them with another water par 3 (which I agree is too similar to the other two, but still a better hole than the one it replaced). As noted, the old 323 yard par 4 with its "Elanor's Peals" bunker scheme works just as well on a long par 5, which did require some fw cut and can still be blind for short hitters. It is still tight as a par 5 to boot.
Packard also removed the snap slice 18th and made it a longer, straighter hole. The 18th is one Palmer complained about, and I think the USGA said it had to be changed to host another event.
And, lastly, Rees took out the snap hook on 16 (old 13) and as a result, reintroduced a short par 4 to the back nine, with more strategy than existed on the old 15 which wasn't driveable.
You may not like the course, but as a former Chicagoan, I think it holds up just fine to other NE courses that have held the Open. I am not quite sure why others of similar width don't come in for equal criticisms as No. 3, to be honest. As to no holes really standing out, I have to ask what holes stand out at courses like Brookline, WF, and Baltusrol? They all strike me as solid all the way around with few stand out holes (with WF having the most IMHO) For that matter, all of those plus Oakmont are slogs under US Open conditions to about the same degree.