Does including extended material in FTL make it more difficult to complete the game?

I ask because I previously completed it on PC before the new material came out, but I've since been playing it on iPad with the new material (i.e. new races, systems, etc) and I am unable to get past the first boss stage, despite trying various strategies over about 10 attempts - 4 of which have got to the final boss.

My only theory on this is that the increased variation in the game means there's more to contend with, so the game is harder, meaning you're less prepared for the final boss.

Yes and no. While advanced edition adds increased variation in the game to deal with, it also enables a greater number of strategies that can be used to reach the final boss. I especially enjoy using the new mind control system as it allows for an additional way of capturing enemy ships intact.

One very specific case where it makes the game harder has to do with the final boss:

His first form now has a hacking device and his last form has mind control.

Though the use of MC has given me a better chance at beating the boss since it makes killing the ship's crew that much easier once you disable his dangerous weapons. This involves using MC on a crew and teleporting him back to your ship to greet your waiting mantis. This completely nullifies his level 3 medbay and overwhelming numbers.