The thing is Latios/as don't stay on one ROUTE, It is like the Legendary Dogs in the GSC series, though the dogs moved everywhere on the region, the Lati's like to stay in a certain area. They are a pain to catch so here is some advice...
Make sure you have these Pokemon with these moves.
At least one Trapinch with the ability called Arena Trap. Make sure it is lvl40. ALL Pokemon are to be under Lvl 40 or the Repels will not work.
A Pokemon that knows surf.
A Pokemon that knows fly.
A Pokemon that knows Sweet Scent. The Pokemon Tropius is good for this as it can learn both Fly and it naturally knows Sweet Scent.
And some Repels, stat-restoring items like potions, full heal.
I did this in Sapphire and it worked just fine, but I think you should stay in the area of Maulville City, Fortree City and The city with the big "Mall". :P Forgot the name of the place but you know where I mean.
Yea, search around those areas, every time you change routes, so does Latias, so sometimes use fly to get to Fortree City to trick the A.I (Does not work all the time) and go left or right to the grass. It is hard... It can take minutes, days, weeks and even months, but keep trying.