I think many previous posts have pretty much summed up Salamence's effect on the game. It puts an end to the endless paint by numbers of switching to counters and draws a line in the sand for a decisive showdown. There are few options for a Pokemon that the defender can switch in to survive any move from any variant of Salamence. However, the Salamence user is under pressure as well because it cannot afford to switch willy-nilly and needs to make Salamence do something for his team before it faints or is forced out.
People who do not like to predict do not use Salamence. However, in facing it, you are taken out of your comfort zone because predict you must. So in a sense, I can understand the desire to get rid of that impediment to "countering everything". However, even with a prediction mistake a good player will seldom lose his whole team to a Mence, in my experience. OTOH, I've seen whole teams go down in a whirlpool of Taunts, DDs, and Waterfall flinches from one Gyarados misplay. It's good enough to force stuff that could do without it to carry HP Electric.
My opinion is that the whole aim of competitive Pokemon is to create an unstoppable Pokemon. A static scenario where every Pokemon, even after setting up is easily answered by another is neither desirable nor possible, IMO. Ultimately, during a match we want to create a Pokemon, through whatever legal means, that laughs at all remaining countermeasures. A well played Salamence can aid in this process with it's natural firepower but I have seldom seen it act as a one-man army blowing through entire teams without support. Some of the main factors that check it are intrinsic and environmental rather than due to specific counters. However that's fine, IMO, as it elevates the game beyond endless repetition of the same countering tactic.
On a side note, I think the current OU is very healthy in terms of Pokemon usage. In April there were about three Pokemon at 20% with Scizor at about 30%. The reason for Scizor's #1 slot is that it checks both Tyranitar and Salamence at numbers 2 and 3 respectively. Whereas Heatran and Gyarados at numbers 4 and 5 act as countervailing forces against Scizor. It's not until about the 20th Pokemon that anything drops below 10% usage which is about the same as UU. Even though we're not discussing this here, I don't see it as overcentralized in the least.
I sometimes say, a bit facetiously, that Palkia should be dropped onto an OU ladder to remind ourselves of what broken is (if it is indeed!). But on a more serious note, maybe auto-banning of titular legends, though convenient, is a bad idea. I'm not sure, but it certainly removes experience that would act as an empirical touchstone for the idea of an Uber.