People choose Thor over Loki (not everyone, but most, as some people like Loki more) because of the bonuses, not minor gods. And who said Thor better than Odin? In my opinion, the 3 best gods are Set, Odin, Thor, closely followed by Loki. People choose Thor 'cause he's versatile. No other civ can go all-dwarf without major econ losses. No other civ can get meteoric mail in classical (that's post-mythic armoury tech). Thor is hard to fight on water because of all hte armoury upgrades and faster gold income.
If that wasn't enough, Thor is the only anti-Set civ because of pig sticker, which works on set animals.
People choose Odin for Jarls (thinks back to Odin FH) and tough husks. Loki for good rushes, but getting weaker as the game goes on (especially when newbs play).
The one thing Thor does need is getting Njord in heroic... but he'd be overpowered if he had that.
To make my point short: People play ____ for:
Odin - good cavalry, awesome FH, best jarls
Thor - gold base econ, very versatile
Loki - good rush, very good ox carts, Nidhogg
And yeah, Loki can be formidable, but he gets weaker as the game goes on, as all the Hersir bonuses get wasted as the armies switch to husk/jarl/rams.
"Three Rings for the Elven-kings under the sky,
Seven for the Dwarf-lords in their halls of stone,
Nine for Mortal Men doomed to die,
One for the Dark Lord on his dark throne
In the Land of Mordor where Shadows lie."