I mean.... if you told us WHICH boss battle you're stuck at then we may be able to help more?
Also, no Megas are in the game until literally the final battle, and that's a gym leader's Pokemon. we probably will have no access to it until E18.
From experience, treeko and grovyle are meh, but when you stick with them and get a Sceptile he is fast, and can one shot one of the bulkiest mons of a boss in the late game. My suggestion is to get a Growlithe from the police quest, but I'm not exactly sure what point you are at in the game so I cant give exact advice.