Alright here we go.
Problems
1 Stead Fast and Cheap units. Stead fast makes cheap low cost troops like skaven slaves way too good for there cost. Stead fast works properly when its in use with costly troops. Because that is more in line with the spirit of the idea.

2 Mega spells, currently there are 2 mega spells that truly need some type of "handling" dreaded 13th and dwellers below. Transformation is bad but its not as bad in my two cents as a spell that just wipes out units. At least when your made into a beast you actually have to roll to wound and the target of the combat can get some type of save for the majority of the attacks.

3 Is one I don't think alot of folks will complain about but its been around for a long time. Cannons forming the dreaded 4th template. A line that hits everything, that is the number one reason folks are scared to mount there heros on something epic like a dragon.

Ok these are the problems now for my take on how to answer these problems.

1 Take steadfast and make it be number of combat ranks, not more ranks. Failing that make some sort of system that simply makes it so you don't have 50 2pt models holding up 30 or 40 bad *** fighting types. I am sure there is a more succinct way to answer the stead fast problem. I am not 100% sure what it is but something to do with rank bonuses mattering more again instead of just more ranks period.

2 Simple fixes here, 13th should not work on any character on foot, also included a system where monstrous infantry counts as 3 models instead of 1. So you have to do 3 wounds per model changed over 1 monstrous infantry to a rat. Second dwellers gives look out sirs. There its fixed.

3The cannon fix is as simple as it is needed. Make cannons randomize. IE if your on a dragon, 5-6 hits rider the rest hits beast. Take away the 4th template. We all know there should only be 3 templates in the game not 4. Cannons, I can feel the dwarf and empire hate from here, damn that will keep me warm come December.

Alright that should get the ball rolling and rember folks, I don't claim to have all the answers, just good ones.