So just started Skullgirls and man I'm bad. The tutorial can be a challenge but I think my biggest issue is the way the buttons are presented. Can be a little confusing knowing which coloured buttons on screen matches the controller buttons.
I played the CPU and on sleepwalk I won easily but then I barely just won on Easy. I was confused by moves so just ended practicing my blocking and button smashing.
I've not played it with a pad but configure the buttons to suit you best. The best thing about arcade stick layouts is when you can do 3 punch / 3 kicks in two simple rows.
I think this is why Tekken and MK are good with a pad because they only have 2 of each so suit pad setups. The shoulder buttons are very accessible too.