Personally, I find the level 50 singles mode the easiest. Some tips are to make sure your team covers each others weaknesses if possible, and try to limit the amount of pokemon that are weak against one type. This is especially important as you get a higher streak, as they no longer tell you what pokemon you'll be up against or anything at all about them once you get 28 wins.
Also it can be helpful to look at the stats of the 6 pokemon you get to choose from at the start of each set of 7 battles very carefully, and make sure you have a mix of pokemon with high attack and high special attack (or else something with high defence/ special defence could wreck your team). I think a fair amount of battle factory comes down to luck though, especially the later rounds when they no longer tell you what pokemon your opponents will have.