Yeah I suppose it's similar to the mind-control gimmick in that it's a way to get your character to act in a totally out-of-character way.

I don't mind this one as much though, perhaps because it doesn't tend to be as over-used as the old mind-control one. And I think it's a little more honest than the mind-control, in that at least it's an explicitly different version of your character - in fact, a separate character of its own in the story - that has this completely different persona. It's also more interesting in how it allows you to juxtapose the actual character next to this contrasting counterpart.

So I kind of like this trope, sometimes anyway - the famous Star Trek episode, for example. And I don't know much about the evil JLA, the Crime Syndicate, but from the little I've seen I think they work pretty well.

I agree with you - and I just loved it very much!

Another pain-in-the-butt collection filing concerned Batman. I had a collection that ran from the 1950's thru about 2012. Detective Comics was filed separately among the "D"s. But all other Bat titles would be filed adjacent to each other.

Do you have any idea how many annuals,specials,super spectaculars, one-shots, mini-series, maxi-series, spin-off series, graphic novels, 3D issues, etc etc was published? If you look at Overstreet you find multiple pages of titles.
Crossover comics were another headache.

I think one reason it works well with the JLA vs CS might be because DC's superheroes are traditionally so much more straightforwardly heroic than the Marvel heroes, outside perhaps Captain America, so the contrast between them and their evil Crime Syndicate counterparts is more obvious and striking.

Marvel's characters, heroes and villains, have traditionally been a little more ambiguous - in-group bickering, Spider-Man trying to make money off his new-found powers,  threats such as Arkon or Dormammu sometimes turning out not to be simple representatives of evil, etc, etc. - so an evil/good counterpart doesn't necessarily provide the same sharp kind of sharp contrast you get with Superman, Batman, WW, etc.

One of the few things I think the modern Marvel has gotten right is to carry on this tradition and even take it further, with, for example, recent versions of long-time villains such as Loki or Ares becoming heroes or at least something other than a plain old evil bad guy.

Presumably Wolverine's "evil" twin would be a polite pacifist who goes around healing people.

Bizarro and the CSA are the rare exception for me that work. Even though they are simply mirror opposites of the heroes, they're also fairly unique conceptually. It's not my favorite concept, but it can work for me just as long as it's not overused. I suppose the Maestro Hulk from the future would be another good example. Sure, this is basically an old evil Hulk with a beard, but he's visually interesting and different enough to warrant his existence as a good concept. 

It's not exactly what you mean, but this idea is why I loathed the bone claws retcon.

Wolverine's natural ability is purely pacifistic. He heals. He doesn't shoot lasers out of his eyes, read minds or control the weather. He just heals. The modification of his body by Weapon X wasn't just an abominable disregard for his status as a human being and a mutilation, it was exploiting a pacifist ability to create a living weapon by sticking six knives in his forearms. The contrast is great. Pacifism vs violence. Healing vs destruction. Organic vs inorganic. But when they were retconned into being part of his mutation all along they blew it. Now Wolverine was always an animal and Weapon X just made him moreso. Stupid.