This is Gallow's house rules: http://www.fantasyflightgames.com/edge_foros_discusion.asp?efid=166&efcid=3&efidt=318981
He adds one misfortune per level of defending skill (choose one of WS, Resil., Coord.). And allows the use of expertise dice to be added to an attackers pool as challenge dice (purple). I think that's a solid house rule that makes skill a bit more important in defense, while avoiding a boost to the importance of Agi.
The system as written favours the very strong, unskilled (e.g. str 5, WS:0) fighter over the normal strength, superior skilled (e.g. str 3, WS: 2, specialized) when it comes to raw damage output. Assuming that Reckless cleave with a great weapon is used (1 step into reckless stance) vs 1 challenge die and using the dice probability generator ( http://www.jaj22.org.uk/wfrp/diceprob.html ) I can calculate a mean damage for the action. This is 12.9 for the skilled weakling and 14.1 for the unskilled (including the effect of one boon). The number of crits for the skilled fighter is 0.9, but only 0.1 for the unskilled brute*. To be honest I think the low-strength but skilled combatant is the more dangerous opponent here, just based on the much higher chance of getting a crit. He also has a chance (albeit slim) to cause 4 crits in one swing (double comets will cause 3 crits with Reckless cleave, and 1 boon-activated crit).
*note that the numbers are probably slightly boosted in both cases due to the fact that I've treated boons and successes as independent, which they in reality are not. But this is the same for both fighters so should not affect the comparison.