Enemies are levelled to your level which assumes a certain offensiveskill which you might lack when going two-handed that can make the game harder. Other then that go ahead.
Not really likely to be a problem. Areas are keyed to your level the first time you go there and stay that level forever for that character, plus certain (most?) areas have limits to how low- or high-level they can be, so you're not going to be seeing foes of your own level all the time, everywhere in the world, like you did in Oblivion. My level 70 Khajiit still meets level 1 bandits when he passes by Riverwood.
So keep your best weapon handy in case you need it, but you should be fine using a new weapon type to cross-train when you run into lesser enemies.