I was pondering this question to myself earlier. I haven't played in a few months, but the
last team I used had a SpecsMence and I quickly became a huge fan. As you can see from the date of the RMT though, it was a few weeks before Latias became OU so if I had to do things over now, would I use SpecsLatias over SpecsMence?
In that particular example, I would stay with SpecsMence, definitley.
It's certainly nothing to do with surprise value though - I think too many people are playing up this supposed 'surprise factor' of SpecsMence but in reality the surprise factor rarely buys you much advantage - I don't know about you but when I see a Salamence my default reaction is 'here comes a Draco Meteor.' Obviously there's a chance of a DD (it seems as though MixMence and DDMence are used almost exactly as much as each other - 43.2% use Draco Meteor compared to 43.8% that use Dragon Dance) but DDMence usually come out late in the game so that's at least a rough indication. What I'm saying is something like Hippowdon or Gliscor is very unlikely to be a default switch into a Salamence. It's a lot more likely to be something to absorb a DM that won't care too much if it's x1.5 instead of x1.3. I would
never use SpecsMence for surprise factor because his counters and checks are too similar to the standard MixMence.
I think a massive advantage in Salamence's favor here is his neutrality to Pursuit combined with the fact that Scizor really doesn't like to switch in. This is a frightening contrast to Latias - over 52% of Scizors use Pursuit and all of them love to switch into Latias.
588 Atk 60BP Pursuit vs 4/0 Latias = 78% - 92%
588 Atk 80BP Pursuit vs 4/0 Latias = 103% - 122%
Similar case with Tyranitar who dislikes switching into Salamence for fear of Brick Break on the mix set or a DD EQ but will happily throw his 445 lb frame at almost any Latias.
Another point in Salamence's favor is Intimidate. If I were to use Latias on that team I wouldn't have Intimidate anywhere which is a bad idea in general for a balanced team that doesn't have a dedicated physical wall. It's just a fantastic asset for checking physical sweepers. On the note of physical sweepers, Salamence also has a Bug resistance for what it's worth.
Salamence's SR weakness is annoying but the team in question has a spinner so I'm going to partially overlook that issue. Latias does have a means of dealing with Blissey but it's possible that SpecsMence will be able to grab one or two kills before the opponent even starts making Blissey his default switch-in to Mence. I also don't like how Trick compromises Latias coverage and only allows him one non-Dragon attack. It wouldn't be a huge issue if I had a Magnezone on my team but I don't so blah.
Basically, Latias may have more potential offensively but Salamence can serve a few more roles for the team and using Latias would open up a few weaknesses I could do without. For example, Salamence is a decent check to Scizor and Lucario, Latias increases my weakness to those two Pokemon (Latias is OHKO'd by +2 Extremespeed after SR 41% of the time).
I'm gonna give a very broad answer and say that it depends on the team as I've hopefully shown here.