Go with the first set defninitly (Garbodor, Camerupt, Togekiss, Hunchkrow, Porygon, Gardevoir,), but instead of garbodor I think Skuntank, Seviper, or Scolipede would be much better ones to use out of the available poison types.
Ame, Could you do Mega Shinies? They could be much rarer and would be some random color you choose for each. Like a chartreuse green rapidash or a bright pink zoroark.
yanmega is really only useful in the game if you breed it for mild/rash nature and to have wing attack and ancient power for early evolution and then to help in level up until it gets bug buzz. (trust me from personal experience it was a real headache)
That would be a good reason to skip Numel. lol, Have you considered trying swoobat? Good speed and spatk, early game and gives you the extra flying coverage before you get charizard and then you just save raltz for gallade instead of gardevoir.
Level caps and other info:
http://www.pokemonreborn.com/game/rebornfaq.html
Ground type wise as a replacement for Excadrill, Camerupt is available early and is extremely useful (Numel event).
And I wouldn't worry about wasting experience. There is plenty opportunity in the game to level up and grind.