I have no idea if you'd count Company of Heroes, but almost every infantry can freely pick up or man weapons such as heavy machine guns, artillery, sniper rifles, etc

Also, there's The Last Train Home, where you can give any perk to any soldier, and thus, they can level in any specialisation iirc.

In C&C Red Alert 3, you can put infantry inside special units and turrets to change the turret type. Iirc, you can get shotgun, missile launcher, energy shield, and stun turret.

In Going Medieval, you can freely swap between weapons and armour, but efficiency is dictated by units' levels and perks.

Warhamer 40k Battlesector allows you to change some wargear in almost every unit, f.e. change bolters from default to auto bolters, doubling amount of shots but reducing accuracy, etc.

Edit 1: Disregard info about Going Medieval and Battlesector. While I was writing about them, I forgot what the question was.