Good grist, but I still think people are overly hard on poor Leo. Ron Santo and other Cubs from the 1969 team have said as much. Other than Popovich, they didn't really have that great of a bench, as evidenced by the shuffle in that third outfield position. There was also no viable backup catcher to Randy Hundley, a position that really requires occasional rest. The Wrigley family was still running the team at the time and trying to win a pennant on the cheap. So I think Leo did as well as he could with what he had.The problem is that most of those Cubs, even Santo, eventually admitted as well that overplaying his regulars at all, not to mention mishandling his pitching staff (he had a nasty habit of over-rotating some of his starters, most notably Ferguson Jenkins and Bill Hands, out of turn often enough that they, too, may have been gassed when they were needed most; and, he had a very weary bullpen down the stretch when he needed them the most, though he had at least two capable arms, Hank Aguirre and Ted Abernathy, to back up an exhausted Phil Regan).
Ron Santo was probably the godsend that season, he picked the right time to have the best season of his career and drive in 123 runs. As for a backup catcher, Gene Oliver wasn't much of a hitter but he knew what he was doing behind the plate, he could handle a pitching staff capably enough when you put him there, and he certainly should have been sent out to spell the stubborn Hundley more often than he was.
There were other factors, too. You may or may not remember how many close calls on the bases went against the Cubs. There was a reason for it: Durocher ramped up the ump baiting so ferociously that he alienated nearly every umpiring crew in the National League. Not to acquit the arbiters if they really were taking that out on the Cubs, but baiting them as a matter of routine is going to guarantee you trouble when you need it least.
Whether that would have been enough to overtake the Mets when they got white-hot (I wouldn't quite rate the 1969 Mets over the 1986 Mets but they were a great team) is debatable, if only because the Mets outpitched the Cubs even if you could balance all other factors out between them. Hundley himself said it years later: when the Mets came up, seemingly out of nowhere, with that pitching staff, you just knew these guys weren't kidding anymore.
Beginning with dropping a pair to the Mets on 8-9 September (Jerry Koosman beat Bill Hands; Tom Seaver beat Ferguson Jenkins), the Cubs went 8-14 to season's end. The Mets went 20-5, including a staggering nine-game winning streak (including the clinching game in which Gary Gentry beat Steve Carlton), over the same stretch.
You can get the full story in the two sources I cited earlier. Leo Durocher, an overrated manager, had a lot to answer for when it was all over (including no little clubhouse tension at various points---denouncing players as "quitters" when they turned up injured, compelling no few Cubs to stick it out no matter how badly they were hurting, wasn't exactly the way to manage a team through the thick of the first pennant race they'd seen since the end of World War II) and the Cubs had to settle for being the best team that didn't win.
Leo, on the other hand, was expected to win and came from an era when pitchers were expected to throw complete games and everyday players were expected to play, well, everyday.
The fact that the 1970 Cubs corrected many of these problems showed he learned, albeit too late. Had they been able to maintain something even close to the pitching power of the 1969 team, I think the 1970 team was even better.
I'd also agree with you on the 1986 Mets being better than the 1969 team in terms of raw talent and certainly a better team on paper. But it isn't team people talk much about anymore, partly over a feeling that they got the 1986 Series handed to them by Bill Buckner's famous error (another topic which I could expond upon) but more because the team members featured some pretty poor human beings-- drug users, wife beaters, etc.